diff --git a/GDE2.0_manual.ps b/GDE2.0_manual.ps
deleted file mode 100755
index a9b90c8..0000000
--- a/GDE2.0_manual.ps
+++ /dev/null
@@ -1,6258 +0,0 @@
-%!
-%%Title: "Laser Prep -- The Apple PostScript Dictionary (md)"
-%%Creator: Apple Software Engineering
-%%CreationDate: Thursday, March 19, 1987
-%{appledict version #70 0
-% ) CopyRight Apple Computer, Inc. 1984-89 All Rights Reserved.
-%%EndComments
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-0.25192 0. 32 0.02519 0.(Genetic Data Environment)awidthshow
-86 306 gm
-1.00982 0. 32 0.10098 0.(version 2.0)awidthshow
-113 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.19348 0. 32 0.01934 0.(Table of Contents)awidthshow
-125 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-0.87683 0.(Introduction.........................................................................................)ashow
-125 148 gm
-( )show
-125 504 gm
-(2)show
-137 90 gm
--0.00367 0.(What's New for this Release)ashow
-137 228 gm
-1.01469 0.(.....................................................................)ashow
-137 226 gm
-( )show
-137 504 gm
-(2)show
-149 90 gm
--0.10981 0.(System Requirements)ashow
-149 196 gm
-1.01313 0.(.............................................................................)ashow
-149 193 gm
-( )show
-149 504 gm
-(2)show
-161 90 gm
--0.09104 0.(Note to Motif users)ashow
-161 184 gm
-1.01264 0.(................................................................................)ashow
-161 182 gm
-( )show
-161 504 gm
-(2)show
-173 90 gm
--0.15522 0.(Installing the GDE)ashow
-173 180 gm
-1.01248 0.(.................................................................................)ashow
-173 178 gm
-( )show
-173 504 gm
-(3)show
-185 90 gm
--0.08174 0.(Using the GDE)ashow
-185 164 gm
-1.01188 0.(.....................................................................................)ashow
-185 163 gm
-( )show
-185 504 gm
-(3)show
-197 90 gm
--0.21920 0.(Data Types)ashow
-197 144 gm
-1.01121 0.(..........................................................................................)ashow
-197 143 gm
-( )show
-197 504 gm
-(7)show
-209 90 gm
--0.10195 0.(Menu Functions)ashow
-221 126 gm
--0.16563 0.(File menu)ashow
-221 176 gm
-1.01232 0.(..................................................................................)ashow
-221 173 gm
-( )show
-221 504 gm
-(7)show
-233 126 gm
--0.20724 0.(Edit menu)ashow
-233 176 gm
-1.01232 0.(..................................................................................)ashow
-233 174 gm
-( )show
-233 504 gm
-(9)show
-245 126 gm
-7.54577 0. 32 0.75457 0.(DNA/RNA menu..........................................................................)awidthshow
-245 208 gm
-( )show
-245 504 gm
-(9)show
-257 90 gm
--0.11619 0.(External Functions)ashow
-257 180 gm
-1.01248 0.(.................................................................................)ashow
-257 179 gm
-( )show
-257 504 gm
-(10)show
-269 90 gm
--0.06219 0.(Bug reports/extensions)ashow
-269 200 gm
-1.01332 0.(............................................................................)ashow
-269 199 gm
-( )show
-269 504 gm
-(12)show
-281 90 gm
--0.14102 0.(Acknowledgments)ashow
-281 180 gm
-1.01248 0.(.................................................................................)ashow
-281 178 gm
-( )show
-281 504 gm
-(12)show
-293 90 gm
--0.08592 0.(Appendix A, File Formats)ashow
-293 216 gm
-1.01406 0.(........................................................................)ashow
-293 214 gm
-( )show
-293 504 gm
-(13)show
-305 90 gm
--0.06129 0.(Appendix B, Adding Functions)ashow
-305 240 gm
-1.01536 0.(..................................................................)ashow
-305 239 gm
-( )show
-305 504 gm
-(16)show
-317 90 gm
-5.07019 0. 32 0.50701 0.(Appendix C, External functions..................................................................)awidthshow
-317 240 gm
-( )show
-317 504 gm
-(19)show
-F T cp
-%%Page: ? 2
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(2)show
-99 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.16366 0.(Introduction)ashow
-126 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.00480 0.(The Genetic Data Environment is part of a growing set of programs for manipulating and analyzing)ashow
-137 90 gm
--0.02925 0.("genetic" data.  It differs in design from other analysis programs in that it is intended to be an expandable and)ashow
-148 90 gm
-0.30548 0. 32 0.03054 0.(customizable system, while still being easy to use.)awidthshow
-170 90 gm
--0.03929 0.(There are a tremendous number of publicly available programs for sequence analysis.  Many of these)ashow
-181 90 gm
--0.02575 0.(programs have found their way into commercial packages which incorporate them into integrated, easy to use)ashow
-192 90 gm
-0.00381 0. 32 0.00038 0.(systems.  The goal of the GDE is to minimize the amount of effort required to integrate sequence analysis)awidthshow
-203 90 gm
-0.02471 0. 32 0.00247 0.(functions into a common environment.  The GDE takes care of the user interface issues, and allows the)awidthshow
-214 90 gm
-0.08422 0. 32 0.00842 0.(programmer to concentrate on the analysis itself.  Existing programs can be tied into the GDE in a matter of)awidthshow
-225 90 gm
-0.05676 0. 32 0.00567 0.(hours \(or minutes\) as apposed to days or weeks.  Programs may be written in any language, and still)awidthshow
-236 90 gm
--0.01551 0.(seamlessly be incorporated into the GDE.)ashow
-258 90 gm
-0.15960 0. 32 0.01596 0.(These programs are, and will continue to be, available at no charge.  It is the hope that this system will)awidthshow
-269 90 gm
--0.00163 0.(grow in functionality as more and more people see the benefits of a modular analysis environment.  Users)ashow
-280 90 gm
--0.04074 0.(are encouraged to make modifications to the system, and forward all changes and additions to Steven Smith)ashow
-291 90 gm
--0.07734 0.(at smith@nucleus.harvard.edu.)ashow
-316 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.33660 0. 32 0.03366 0.(What's New for this Release)awidthshow
-339 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02201 0.(There have been several changes made for this 2.0 release of GDE.  The most notable changes involve new)ashow
-350 90 gm
-0.06668 0. 32 0.00666 0.(editing capabilities.  For most functions, the user can either select the sequences by their name, or by)awidthshow
-361 90 gm
--0.06840 0.(dragging over sections of the sequence text.  See editing for more details.  Other added features include a new)ashow
-372 90 gm
--0.07867 0.(checking mode, reduced scale viewing for sequence assembly, improved cut/copy/paste, and many new)ashow
-383 90 gm
-0.08651 0. 32 0.00865 0.(external functions.  There is also a new file format, GDE format, which retains more of the all of the)awidthshow
-394 90 gm
-0.05279 0. 32 0.00527 0.(available information about a sequence.  This format \(unlike Genbank format in GDE1.0\) will not loose)awidthshow
-405 90 gm
-0.02593 0. 32 0.00259 0.(fields such as group numbers, etc.)awidthshow
-427 90 gm
--0.01397 0.(There is one other change that should be noted.  The old "flat" file format has changed.  The format now)ashow
-438 90 gm
-(compresses leading gaps by allowing an offset number in parentheses after the name.  GDE2.0 will still read)show
-449 90 gm
-0.15045 0. 32 0.01504 0.(old "flat" files, but will write them out in the new format.  This might cause difficulties for some external)awidthshow
-460 90 gm
-0.17807 0. 32 0.01780 0.(functions written using this format.  Because of the change, it is VERY important to keep the GDE1.0)awidthshow
-471 90 gm
-0.02624 0. 32 0.00262 0.(support programs separate from GDE2.0, as some are now incompatible.  The original flatfile format can be)awidthshow
-482 90 gm
--0.10980 0.(duplicated using ReadSeq/FastA format and sed.)ashow
-518 90 gm
-14 fz
-2 F /|______Times-Roman fnt
--0.02626 0.(System Requirements)ashow
-541 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.16036 0. 32 0.01603 0.(GDE 2.0 currently runs on the Sun family of workstations.  This includes the Sun3 and Sun4 \(Sparcstation\))awidthshow
-552 90 gm
-0.19104 0. 32 0.01910 0.(systems.  It was written in XView, and runs on Suns using OpenWindows 2.0 or MIT's X Windows.  It)awidthshow
-563 90 gm
-0.00488 0. 32 0.00048 0.(runs in both monochrome, and color, and can be run remotely on any system capable of running X Windows)awidthshow
-574 90 gm
--0.00602 0.(Release 4.  You should have at least 15 meg of free disk space available.)ashow
-596 90 gm
-0.14724 0. 32 0.01472 0.(We are also supporting a DECStation version of GDE.  This is running under XView 3.0/X11R5. We)awidthshow
-607 90 gm
-0.02227 0. 32 0.00222 0.(encourage interested people to port the programs to their favorite Unix platform.  We hope to support the)awidthshow
-618 90 gm
--0.00794 0.(SGI and Cray line of Supercomputers.)ashow
-643 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.36575 0. 32 0.03657 0.(Note to Motif users)awidthshow
-666 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.08575 0. 32 0.00857 0.(GDE2.0 can be run using different window managers.  The most common alternative to olwm is the Motif)awidthshow
-677 90 gm
-0.12878 0. 32 0.01287 0.(window manager \(mwm\).  The only problem in using another window manager is that the status line is not)awidthshow
-688 90 gm
--0.04948 0.(displayed.  We have added a "Message panel" as an option under "File->Properties" which displays all of the)ashow
-699 90 gm
-0.10406 0. 32 0.01040 0.(information contained on the status line.)awidthshow
-F T cp
-%%Page: ? 3
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(3)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03054 0.(People using other window managers may also prefer using xterm, and xedit as default terminals and file)ashow
-92 90 gm
--0.02236 0.(editors.  This can be accomplished by replacing all occurrences of 'shelltool' and 'textedit' with 'xterm -e' and)ashow
-103 90 gm
-0.10833 0. 32 0.01083 0.('xedit' in the $GDE_HELP_DIR/.GDEmenus file.)awidthshow
-128 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.33935 0. 32 0.03393 0.(Installing the GDE)awidthshow
-151 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03640 0.(Instructions for the source code release are included in the README.install file.)ashow
-173 90 gm
--0.00282 0.(The binary installations consist of creating a GDE directory, such as /usr/local/GDE, and un-taring the)ashow
-184 90 gm
-0.15594 0. 32 0.01559 0.(installation tarfile into the directory.  If you are installing the GDE for your own use, then you can simply)awidthshow
-195 90 gm
-0.01647 0. 32 0.00164 0.(make a GDE subdirectory.  There is no need to be superuser \(root\) to do the installation in your own)awidthshow
-206 90 gm
--0.02723 0.(directory.  For example:)ashow
-225 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
-0.69610 0. 32 0.06961 0.(demo% )awidthshow
-1 fs
-{}mark T /Courier-Bold /|______Courier-Bold 0 rf
-2 F /|______Courier-Bold fnt
-1.28005 0. 32 0.12800 0.(mkdir /usr/local/GDE)awidthshow
-233 90 gm
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
-0.79788 0. 32 0.07978 0.(demo% )awidthshow
-1 fs
-{}mark T /Courier-Bold /|______Courier-Bold 0 rf
-2 F /|______Courier-Bold fnt
-1.26770 0. 32 0.12677 0.(cp GDE2.0.tar /usr/local/GDE)awidthshow
-241 90 gm
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
-0.55816 0. 32 0.05581 0.(demo% )awidthshow
-1 fs
-{}mark T /Courier-Bold /|______Courier-Bold 0 rf
-2 F /|______Courier-Bold fnt
-0.97320 0. 32 0.09732 0.(cd /usr/local/GDE)awidthshow
-249 90 gm
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
-0.65994 0. 32 0.06599 0.(demo% )awidthshow
-1 fs
-{}mark T /Courier-Bold /|______Courier-Bold 0 rf
-2 F /|______Courier-Bold fnt
-0.85617 0. 32 0.08561 0.(tar -xf GDE2.0.tar)awidthshow
-271 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.00643 0.(After this, each new user will need to add two lines to their .cshrc file so that they can find the gde programs)ashow
-282 90 gm
--0.07226 0.(and files.)ashow
-301 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
-0.50384 0. 32 0.05038 0.(demo% )awidthshow
-1 fs
-{}mark T /Courier-Bold /|______Courier-Bold 0 rf
-2 F /|______Courier-Bold fnt
-0.59280 0. 32 0.05928 0.(cat >> ~/.cshrc)awidthshow
-309 90 gm
-1.39968 0. 32 0.13996 0.(set path = \($path /usr/local/GDE/bin\))awidthshow
-317 90 gm
-2.04071 0. 32 0.20407 0.(setenv GDE_HELP_DIR /usr/local/GDE/help/)awidthshow
-325 90 gm
-0.60202 0.(^D)ashow
-344 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.06118 0. 32 0.00611 0.(You may wish to make a copy of the .GDEmenus file from the help directory into your home directory.)awidthshow
-355 90 gm
-0.13107 0. 32 0.01310 0.(This is only necessary if you wish to modify your menus.  Copy the demo files from /usr/local/GDE/demo)awidthshow
-366 90 gm
--0.02130 0.(into your local directory, and you are now ready to use the GDE.)ashow
-388 90 gm
--0.05734 0.(FastA and Blast need to have the properly formatted databases installed in the $GDE_HELP_DIR under the)ashow
-399 90 gm
-0.15838 0. 32 0.01583 0.(directories FASTA/PIR, FASTA/GENBANK, BLAST/pir BLAST/genbank.  For FASTA, simply copy a)awidthshow
-410 90 gm
--0.01397 0.(version of PIR and Genbank into the proper directory.  Alternately,  the PIR and GENBANK files can be)ashow
-421 90 gm
-0.08224 0. 32 0.00822 0.(symbolic links to copies of Genbank held elsewhere on your system.)awidthshow
-443 90 gm
-0.01754 0. 32 0.00175 0.(Blast installation involves converting PIR and GENBANK to a temporary FASTA format \(using pir2fasta)awidthshow
-454 90 gm
--0.07652 0.(and gb2fasta\) and then using pressdb for nucleic acid, and setdb for amino acid to reformat the databases again)ashow
-465 90 gm
-0.23468 0. 32 0.02346 0.(into blast format.  The .GDEmenus file is currently set up to search with blast using the following)awidthshow
-476 90 gm
-0.01464 0. 32 0.00146 0.(databases: pir, genpept, genupdate, and genbank.  If you wish to divide these into subdivisions, then the)awidthshow
-487 90 gm
--0.00154 0.(.GDEmenus file will have to be edited.)ashow
-509 90 gm
-0.18249 0. 32 0.01824 0.(The most up to date release of blast can be obtained via anonymous ftp to ncbi.nlm.nih.gov.  The most)awidthshow
-520 90 gm
--0.02844 0.(recent release of FASTA can be obtained via anonymous ftp to uvaarpa.virginia.edu.)ashow
-545 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.21560 0. 32 0.02156 0.(Using the GDE)awidthshow
-568 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.08346 0. 32 0.00834 0.(It is assumed that the user is familiar with the Unix, and OpenWindows/Xwindows environments.  It is also)awidthshow
-579 90 gm
--0.04437 0.(assumed that people running standard MIT X-Windows will be using the OpenLook window manager)ashow
-590 90 gm
-0.03479 0. 32 0.00347 0.(\(olwm\).  Other window managers work with varied success.  If you are not certain as to how your system is)awidthshow
-601 90 gm
-0.06744 0. 32 0.00674 0.(set up, please contact your systems administrator.)awidthshow
-623 90 gm
--0.00114 0.(Once the window system has started, and a terminal window \(xterm, shelltool etc.\) you can start up the GDE)ashow
-634 90 gm
-0.61325 0. 32 0.06132 0.(by typing:)awidthshow
-656 90 gm
-1.45217 0. 32 0.14521 0.(demo% )awidthshow
-1 fs
-{}mark T /Times-Bold /|______Times-Bold 0 rf
-2 F /|______Times-Bold fnt
-1.81137 0. 32 0.18113 0.(gde tRNAs)awidthshow
-678 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-2 F /|______Times-Roman fnt
--0.00747 0.(This should load the sample data set tRNAs into GDE, and the following window should appear:)ashow
-F T cp
-%%Page: ? 4
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(4)show
-0 0 gm
-(nc 72 90 269 544 6 rc)kp
-64 gr
-112 136 243 419 1 rc
-0 gr
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-82 245 gm
-(nc 73 244 85 330 6 rc)kp
-0 gr
-T 1 setTxMode
-2 F /|______Times-Roman fnt
--0.11044 0.(Command menus)ashow
-256 425 gm
-(nc 247 424 259 474 6 rc)kp
--0.07157 0.(Scrollbars)ashow
-247 144 gm
-(nc 238 143 250 195 6 rc)kp
--0.13261 0.(Status line)ashow
-184 92 gm
-(nc 175 91 199 123 6 rc)kp
-(Short)show
-196 92 gm
--0.16336 0.(names)ashow
-85 416 gm
-(nc 76 415 100 464 6 rc)kp
--0.13940 0.(Sequence)ashow
-97 416 gm
--0.24850 0.(alignment)ashow
-(nc 72 90 269 544 6 rc)kp
-pr
-140 195 pl
-129 186 pl
-127 189 pl
-126 192 pl
-140 195 pl
-0 gr
-1 ep
-94 172 gm
-127 189 0 gr
-lin
-pr
-157 361 pl
-145 368 pl
-147 371 pl
-150 373 pl
-157 361 pl
-1 ep
-103 415 gm
-147 371 0 gr
-lin
-pr
-184 397 pl
-196 406 pl
-197 403 pl
-198 399 pl
-184 397 pl
-1 ep
-247 424 gm
-197 403 0 gr
-lin
-pr
-229 325 pl
-228 340 pl
-232 339 pl
-235 338 pl
-229 325 pl
-1 ep
-247 424 gm
-232 339 0 gr
-lin
-pr
-166 136 pl
-178 129 pl
-176 126 pl
-173 124 pl
-166 136 pl
-1 ep
-184 118 gm
-176 126 0 gr
-lin
-94 137 gm
-(nc 85 136 97 170 6 rc)kp
-0 gr
-T 1 setTxMode
-(Cursor)show
-265 218 gm
-(nc 256 217 268 327 6 rc)kp
--0.10447 0.(Split screen drag point)ashow
-(nc 72 90 269 544 6 rc)kp
-pr
-225 384 pl
-235 373 pl
-232 372 pl
-228 370 pl
-225 384 pl
-0 gr
-1 ep
-256 325 gm
-232 372 0 gr
-lin
-167 472 gm
-(nc 158 471 170 543 6 rc)kp
-0 gr
-T 1 setTxMode
--0.16412 0.(Scroll elevator)ashow
-(nc 72 90 269 544 6 rc)kp
-pr
-148 397 pl
-147 412 pl
-151 411 pl
-154 410 pl
-148 397 pl
-0 gr
-1 ep
-161 465 gm
-151 411 0 gr
-lin
-pr
-129 228 pl
-115 229 pl
-116 232 pl
-117 236 pl
-129 228 pl
-1 ep
-84 243 gm
-116 232 0 gr
-lin
-131 460 gm
-(nc 122 459 134 515 6 rc)kp
-0 gr
-T 1 setTxMode
--0.13102 0.(Resize tabs)ashow
-(nc 72 90 269 544 6 rc)kp
-pr
-119 401 pl
-118 416 pl
-122 415 pl
-125 414 pl
-119 401 pl
-0 gr
-1 ep
-129 454 gm
-122 415 0 gr
-lin
-pr
-229 399 pl
-215 404 pl
-217 407 pl
-220 410 pl
-229 399 pl
-1 ep
-164 445 gm
-217 407 0 gr
-lin
-153 454 gm
-137 465 lin
-300 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-10 fz
-2 F /|______Times-Roman fnt
-0.08865 0. 32 0.00886 0.(This is the sequence alignment editor.  It consists of a color alignment display, a set of command menus,)awidthshow
-311 90 gm
-0.00823 0. 32 0.00082 0.(horizontal and vertical scroll bars to navigate the alignment, a list of short sequence names \(usually the)awidthshow
-322 90 gm
-0.02410 0. 32 0.00241 0.(LOCUS of a Genbank entry\), and a status line.  The cursor is located in the upper left corner.)awidthshow
-355 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.07032 0.(Using the Mouse)ashow
-378 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02319 0.(The mouse follow OpenLook standards for operation.  The functions for each button are:)ashow
-0 0 gm
-(nc 391 90 498 329 6 rc)kp
-64 gr
-411 178 497 239 17.5 17.5 1 rr
-0 gr
-411.5 178.5 496.5 238.5 17.5 17.5 0 rr
-64 gr
-426 189 460 197 17.5 17.5 1 rr
-0 gr
-426.5 189.5 459.5 196.5 17.5 17.5 0 rr
-64 gr
-426 205 460 212 17.5 17.5 1 rr
-0 gr
-426.5 205.5 459.5 211.5 17.5 17.5 0 rr
-64 gr
-426 220 460 227 17.5 17.5 1 rr
-0 gr
-426.5 220.5 459.5 226.5 17.5 17.5 0 rr
-142 315 107 239 th
-441 92 gm
-tu
-(nc 434 91 443 153 6 rc)kp
-ts
-0 gr
-T 1 setTxMode
-12 fz
-2 F /|______Times-Roman fnt
--0.24205 0.(Object selection)ashow
-tu
-ts
-450 92 gm
-tu
-(nc 443 91 452 165 6 rc)kp
-ts
--0.14672 0.(clicking & dragging)ashow
-tu
-ts
-441 270 gm
-tu
-(nc 434 269 443 328 6 rc)kp
-ts
--0.20312 0.(Menu selection)ashow
-tu
-ts
-450 270 gm
-tu
-(nc 443 269 452 302 6 rc)kp
-ts
--0.09335 0.(dragging)ashow
-tu
-441 151 gm
-(nc 391 90 498 329 6 rc)kp
-441 189 0 gr
-lin
-433 182 449 198 165 195 1 ar
-441 265 gm
-441 231 lin
-433 224 449 239 345 375 1 ar
-ts
-399 186 gm
-tu
-(nc 392 186 401 237 6 rc)kp
-ts
-0 gr
-T 1 setTxMode
--0.22036 0.(Object adjust)ashow
-tu
-403 208 gm
-(nc 391 90 498 329 6 rc)kp
-426 208 0 gr
-lin
-418 201 434 217 255 285 1 ar
-518 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-10 fz
-2 F /|______Times-Roman fnt
-0.01296 0. 32 0.00129 0.(The left mouse button is used for placing the cursor, selecting sequences by their short)awidthshow
-529 90 gm
-0.16891 0. 32 0.01689 0.(names, scrolling/paging, performing split screens, and resizing.  The right button is used for pop up menus,)awidthshow
-540 90 gm
--0.01223 0.(and scrollbar menus.  The middle button is used for extending a text selection.)ashow
-562 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.11749 0.(Cursor Movement)ashow
-585 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-(The cursor can be moved using the arrow keys, or by clicking the mouse within a sequence.  The cursors)show
-596 90 gm
-0.14465 0. 32 0.01446 0.(position is displayed on the status line in both sequence position and alignment column number.  The right)awidthshow
-607 90 gm
-0.06561 0. 32 0.00656 0.(hand side of the status line shows the left and right column positions of the currently active display.)awidthshow
-629 90 gm
-0.07385 0. 32 0.00738 0.(Scrolling is controlled by the scrollbar elevator.  By clicking \(left mouse button\) on one of the elevator)awidthshow
-640 90 gm
--0.03851 0.(arrows, the screen will scroll one character in that direction.  By dragging the elevator center, the screen can)ashow
-651 90 gm
--0.00059 0.(be moved directly to any location.  By clicking directly to one side of the elevator, the screen will scroll one)ashow
-662 90 gm
-0.07583 0. 32 0.00758 0.(full screen in that direction.  And by clicking on the scrollbar anchor, the elevator will move to that anchor.)awidthshow
-673 90 gm
-0.20538 0. 32 0.02053 0.(Scrollbars also have menus associated with them giving other scroll options.  Use the right mouse button to)awidthshow
-684 90 gm
-(activate the menu.)show
-F T cp
-%%Page: ? 5
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(5)show
-92 90 gm
--0.12741 0.(Selecting Sequences)ashow
-115 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.05250 0.(Sequence selection is necessary before most functions can be performed.  Selecting sequences is)ashow
-126 90 gm
--0.03315 0.(accomplished by clicking or dragging \(left button\) over the short name associated with the sequence\(s\).  The)ashow
-137 90 gm
--0.01461 0.(name of the sequence should become highlighted on the release of the mouse button.  By holding down the)ashow
-148 90 gm
-0.13977 0. 32 0.01397 0.(shift key, you can toggle the selection on or off for any set of sequences.  By clicking just to the right of)awidthshow
-159 90 gm
--0.00563 0.(any sequence short name, you will deselect all of them.)ashow
-181 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.20321 0.(Selecting Text)ashow
-204 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.00436 0.(Selecting text is accomplished in much the same way as selecting entire sequences.  In the editing window,)ashow
-215 90 gm
-0.04013 0. 32 0.00401 0.(you can drag the mouse pointer over a rectangular region the select a block of text.  By using the shift key)awidthshow
-226 90 gm
--0.01466 0.(\(or the middle mouse button\) you can adjust the selection to include other sequences, or other columns of)ashow
-237 90 gm
--0.01264 0.(text.  If groups are enabled, GDE will automatically select all sequences in a group if any one sequence in a)ashow
-248 90 gm
--0.07606 0.(group is selected \(See Sequence Editing\).)ashow
-270 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.12741 0.(Sequence Protection)ashow
-293 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.05520 0.(All sequences can be individually protected against accidental modification.  This is accomplished by)ashow
-304 90 gm
--0.01127 0.(selecting the set of sequences that you are interested in editing, and choosing the "Set protections" menu)ashow
-315 90 gm
-0.03738 0. 32 0.00373 0.(item under the File menu.  Your choices are:)awidthshow
-337 90 gm
--0.03042 0.(Unambiguous modification)ashow
-337 306 gm
--0.13563 0.(Changing/adding/deleting regular characters)ashow
-348 90 gm
--0.02313 0.(Ambiguous changes)ashow
-348 306 gm
-0.28198 0. 32 0.02819 0.(Changing ambiguous codes \('N', 'X'...\))awidthshow
-359 90 gm
--0.01168 0.(Alignment modifications)ashow
-359 306 gm
-0.23391 0. 32 0.02339 0.(Changing alignment gaps \('-', '~'\))awidthshow
-381 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.15385 0.(Sequence Editing)ashow
-404 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.04483 0.(Sequences can be edited by simply typing to insert, and using the delete or backspace key to delete characters.)ashow
-415 90 gm
-0.05371 0. 32 0.00537 0.(Sequences must have the proper protections set to allow the type of modifications that you are attempting.)awidthshow
-426 90 gm
-0.06790 0. 32 0.00679 0.(The default protection level only allows modification to the alignment, but not to the sequences themselves.)awidthshow
-437 90 gm
--0.00852 0.(The Sun function keys, cut, copy and paste are used to edit selected text.  Text selections work in rectangular)ashow
-448 90 gm
-(\(possibly disjointed\) regions.  You can cut or copy a block of sequence text, and paste it to a new cursor)show
-459 90 gm
-0.10787 0. 32 0.01078 0.(location using these three keys.)awidthshow
-F T cp
-%%Page: ? 6
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(6)show
-92 90 gm
--0.11007 0.(Repeat Counts)ashow
-115 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02497 0.(By typing a numeric value before an editing function you can insert, delete or move a number of characters at)ashow
-126 90 gm
--0.00587 0.(a time.  The current repeat count is displayed on the status line, and can be cleared by clicking the left mouse)ashow
-137 90 gm
-0.08789 0. 32 0.00878 0.(button in the alignment window.  In order to insert twenty gaps into a sequence, one would type "20-".  In)awidthshow
-148 90 gm
--0.02253 0.(order to move down five sequences, one would type "5)ashow
-{}mark F /Symbol /|______Symbol 0 rf
-7 fz
-2 F /|______Symbol fnt
-(\257)show
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.02194 0.(".  This works with all sequence types, however the)ashow
-159 90 gm
--0.01254 0.(meta \(diamond\) key must be held down when the cursor is in a text or mask sequence.  This is because)ashow
-170 90 gm
--0.07215 0.(numbers are valid characters in these sequences, and would otherwise be confused with repeat counts.)ashow
-192 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.11955 0.(Split Screen)ashow
-215 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.11734 0. 32 0.01173 0.(Split screen editing allows the viewing one region while editing another.  This is very useful for aligning)awidthshow
-226 90 gm
--0.03680 0.("downstream" regions by editing "upstream".)ashow
-248 90 gm
-0.14480 0. 32 0.01448 0.(The alignment window can be split horizontally into two or more windows into the alignment.  These)awidthshow
-259 90 gm
--0.03460 0.(windows scroll independently of each other both horizontally and vertically.  The short names displayed to)ashow
-270 90 gm
--0.01350 0.(the left of the alignment correspond to the window that was last scrolled or edited.  Care should be taken in)ashow
-281 90 gm
--0.04472 0.(any modifications done in this mode so that edits are performed on the correct sequence.  To avoid confusion)ashow
-292 90 gm
-0.00595 0. 32 0.00059 0.(during split screen operations, the vertical scroll bars may be locked so that all windows scroll together.)awidthshow
-0 0 gm
-(nc 294 162 447 412 6 rc)kp
-64 gr
-295 163 415 411 1 rc
-0 gr
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-rh
-psb
-pse
-0 0 2 9 9 2 dh
-419 314 gm
-425 307 lin
-rh
-psb
-pse
-0 0 pen
-400 238 gm
-400 238 lin
-nc ct 39 0 put
-pr
-409 256 pl
-400 238 pl
-418 247 pl
-409 256 pl
-1 ep
-1 1 pen
-409 256 gm
-bp
-400 238 T qi
-400 238 qc
-418 247 qc
-418 247 qc
-409 256 qc
-409 256 48 gr
-T qq
-qf
-qf
-ef
-15 ec
-(nc 294 162 447 412 6 rc)kp
-2 2 pen
-408 246 gm
-417 255 lin
-0 0 pen
-401 306 gm
-401 306 lin
-nc ct 39 0 put
-pr
-410 324 pl
-401 306 pl
-419 315 pl
-410 324 pl
-0 gr
-1 ep
-1 1 pen
-410 324 gm
-bp
-401 306 T qi
-401 306 qc
-419 315 qc
-419 315 qc
-410 324 qc
-410 324 0 gr
-T qq
-qf
-qf
-ef
-15 ec
-(nc 294 162 447 412 6 rc)kp
-2 2 pen
-409 314 gm
-418 323 lin
-1 1 pen
-467 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-2 F /|______Times-Roman fnt
-0.05432 0. 32 0.00543 0.(In order to split a window into two views, grab \(left button\) the left or right anchor \(small rectangle\) at)awidthshow
-478 90 gm
--0.02000 0.(either end of the horizontal scrollbar and drag to the middle of the window.  This should split the window)ashow
-489 90 gm
-0.21789 0. 32 0.02178 0.(into two views.  To join two views, place the mouse pointer on the horizontal scroll bar use the menu \(right)awidthshow
-500 90 gm
-0.61981 0. 32 0.06198 0.(button\) .)awidthshow
-522 90 gm
-(The views are NOT two copies of the alignment.  Changes in one window are reflected in the other.  Users)show
-533 90 gm
-0.00976 0. 32 0.00097 0.(should not be confused by this fact.)awidthshow
-555 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.06040 0.(Sequence Grouping)ashow
-578 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.00846 0.(Sequences can be grouped for editing functions.  This is very helpful when trying to adjust several sub)ashow
-589 90 gm
--0.00823 0.(alignments.  When grouped, all sequences within a group will be affected by editing in any member of the)ashow
-600 90 gm
-0.07675 0. 32 0.00767 0.(group.  All sequences within a group must have protections set to allow modification before any one will be)awidthshow
-611 90 gm
--0.20011 0.(modified.)ashow
-633 90 gm
--0.03013 0.(In order to group sequences, select the names of the sequences that should fall within a group, and select)ashow
-644 90 gm
--0.02406 0.(Group under the Edit menu.  A number will be placed at the left of the sequence representing its assigned)ashow
-655 90 gm
--0.04641 0.(group number.  To any sequence or sequences, the user selects those sequences and uses the Ungroup)ashow
-666 90 gm
--0.06661 0.(command under the Edit menu.)ashow
-688 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.11912 0.(Special keys)ashow
-F T cp
-%%Page: ? 7
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(7)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.01528 0.(There are also a few special function keys used in the GDE.  Some functions have meta key equivalences so)ashow
-92 90 gm
--0.01637 0.(that they can be called from the keyboard, instead of by the menu system.  The "meta" key is a standard)ashow
-103 90 gm
--0.05270 0.(property of X windows, and may be remapped to a different key symbol for different keyboards.  For)ashow
-114 90 gm
-0.11459 0. 32 0.01145 0.(example, meta on Sun workstations is represented with a )awidthshow
-{}mark F /Symbol /|______Symbol 0 rf
-9 fz
-2 F /|______Symbol fnt
-(\340)show
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.11154 0. 32 0.01115 0.(, where on a Macintosh running MacX it might)awidthshow
-125 90 gm
-0.13610 0. 32 0.01361 0.(be the "apple" key.  The operation of the key is the same as the control or shift key, it is held down while)awidthshow
-136 90 gm
--0.04826 0.(pressing the second key in the sequence.)ashow
-158 90 gm
-0.07690 0. 32 0.00769 0.(Cut text, copy text and paste text are mapped to the Openlook equivalent keys \(L10, L6, and L8 on Sun)awidthshow
-169 90 gm
--0.03259 0.(keyboards\).  Other meta keys are defined in the .GDEmenus file, and may be changed to suit your)ashow
-180 90 gm
--0.23315 0.(preferences.)ashow
-205 90 gm
-14 fz
-2 F /|______Times-Roman fnt
--0.01499 0.(Data Types)ashow
-228 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.01342 0. 32 0.00134 0.(The GDE supports several data types.  The data types supported in 2.0 are DNA, RNA, protein \(single letter)awidthshow
-239 90 gm
--0.08953 0.(codes\), mask sequence, and text.)ashow
-261 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.16458 0.(DNA and RNA)ashow
-284 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.06896 0.(Nucleic acid sequences are tightly type cast, and can contain any IUPAC code \(ACGTUM RSVWYHKDBN\))ashow
-295 90 gm
-0.00411 0. 32 0.00041 0.(as well as two alignment gap characters \('~' and '-'\).  Some keys are remapped to fit IUPAC codes.  For)awidthshow
-306 90 gm
-0.00274 0. 32 0.00027 0.(example,  'X' is mapped to 'N'.  All nonstandard characters get mapped to the alignment gap '-'.  Upper and)awidthshow
-317 90 gm
--0.06726 0.(lower case are both supported, and the T/U characters are mapped based on whether you are working with)ashow
-328 90 gm
--0.01962 0.(DNA or RNA.  The color coding for DNA and RNA is identical.  The color for ambiguous characters, and)ashow
-339 90 gm
-0.16555 0. 32 0.01655 0.(for alignment gaps is grey.)awidthshow
-361 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.20167 0.(Amino Acid Sequence)ashow
-384 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.04162 0.(Amino acid sequences are loosely type cast, and can contain any valid ASCII character.  The results of)ashow
-395 90 gm
--0.09436 0.(analysis on nonstandard characters is not guaranteed. The color for nonstandard amino acid characters, and for)ashow
-406 90 gm
-0.24002 0. 32 0.02400 0.(alignment gaps is grey.)awidthshow
-428 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.16378 0.(Text Sequence)ashow
-451 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03298 0.(Any valid ASCII printable character can be entered into a text sequence.  Care should be taken with using)ashow
-462 90 gm
--0.00344 0.(space characters, as these will only be saved properly in Genbank format, and not in flat file format.  The)ashow
-473 90 gm
--0.04928 0.(characters @#% and " should be avoided as well, as these can confuse the reading of flat files if saved in that)ashow
-484 90 gm
--0.02505 0.(format.)ashow
-506 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.13627 0.(Mask Sequence)ashow
-529 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03303 0.(Mask sequence is identical to text sequence with the following exceptions.  Mask sequence can have the)ashow
-540 90 gm
-0.06149 0. 32 0.00614 0.(ability \(function dependent\) of masking out positions in an alignment for analysis.  If a mask sequence is)awidthshow
-551 90 gm
-0.01480 0. 32 0.00148 0.(selected along with some other sequence\(s\) for an analysis function that permits masking, then all columns)awidthshow
-562 90 gm
-0.06927 0. 32 0.00692 0.(that contain a '0' in the mask sequence will be ignored by the function.  The mask itself would not be passed)awidthshow
-573 90 gm
-0.22354 0. 32 0.02235 0.(to the analysis function either.  Some functions allow masking, some do not.  Refer to the instruction page)awidthshow
-584 90 gm
--0.00167 0.(for each function to see whether or not it supports sequence masking.)ashow
-606 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.06585 0.(Color Masks)ashow
-629 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.01022 0. 32 0.00102 0.(Color masks give color to a sequence on a position by position basis.  Individual sequences can have color)awidthshow
-640 90 gm
--0.01266 0.(masks attached to them, or one color mask can be used for an entire alignment.  Color masks are generated)ashow
-651 90 gm
--0.00192 0.(externally by some analysis functions, and are then passed back to the GDE.  The file format for a colormask)ashow
-662 90 gm
--0.07350 0.(is described in Appendix A.)ashow
-698 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.15777 0. 32 0.01577 0.(Menu Functions: File menu)awidthshow
-F T cp
-%%Page: ? 8
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 303 gm
-12 fz
-2 F /|______Times-Roman fnt
-(8)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.00126 0.(The GDE has several built-in menu functions under the File and Edit menus.  These functions are unique in)ashow
-92 90 gm
--0.02758 0.(that they are part of the primary display editor, and are not described in the .GDEmenus file.)ashow
-126 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-0.33511 0.(Open...)ashow
-138 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.19515 0. 32 0.01951 0.(Selecting this will bring up the open file dialog box.  Users can scroll through a list of files in the current)awidthshow
-149 90 gm
--0.07145 0.(directory, move up and down the directory tree, and open any individual data file.  The sequence data in that)ashow
-160 90 gm
--0.02137 0.(file is loaded into the current editing window below any existing sequences.  The open command will open)ashow
-171 90 gm
--0.01487 0.(any Genbank formatted file, or a GDE flat file.)ashow
-193 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-1.41235 0. 32 0.14123 0.(Save as...)awidthshow
-205 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.07537 0. 32 0.00753 0.(This function will save the entire alignment to a specified file in either Genbank or flat file format.  The file)awidthshow
-216 90 gm
--0.00964 0.(will be saved in the local directory unless a relative or absolute path is specified.)ashow
-249 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-0.19628 0.(Properties...)ashow
-261 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.02334 0. 32 0.00233 0.(Properties controls the display settings.  Those settings include character size, color type,  and insert)awidthshow
-272 90 gm
--0.07415 0.(direction.  The screen can also be inverted, vertical scroll lock and keyboard clicks \(tactile feedback\) can be)ashow
-283 90 gm
-0.11657 0. 32 0.01165 0.(turned on or off.    Vertical scrollbar lock will cause all split views to scroll together in the vertical)awidthshow
-294 90 gm
--0.11550 0.(direction.)ashow
-0 0 gm
-(nc 296 234 431 370 6 rc)kp
-64 gr
-297 235 430 369 1 rc
-0 gr
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-354 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02021 0.(Select all sequences containing a given string in their short names field.  No wild cards are allowed, and only)ashow
-365 90 gm
--0.01213 0.(selecting is allowed, not de-selecting.  The search is started when the Return key is pressed, and multiple)ashow
-376 90 gm
--0.06175 0.(searches can be accumulated.  Press Done when finished.)ashow
-398 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.08575 0.(Cut/Copy/Paste sequences)ashow
-410 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.05426 0.(Cut copy and paste are primarily useful for reordering sequences, and for making duplicate copies of a given)ashow
-421 90 gm
-0.07507 0. 32 0.00750 0.(sequence.  They do not pass information to other programs.  This capability will be implemented in a later)awidthshow
-432 90 gm
--0.04278 0.(release.  Cut and copy will place the selected sequences on an internal clipboard.  They can then be pasted)ashow
-443 90 gm
--0.06423 0.(back into the top of editing window \(default\) or under the last selected sequence.)ashow
-465 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-0.02943 0.(Group/Ungroup)ashow
-477 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.00544 0.(Assign a group number to the selected sequences.  Edit operations in any one sequence within the group will)ashow
-488 90 gm
-0.00320 0. 32 0.00032 0.(be propagated to all within the group.  Sequence protections from one group are also imposed upon all other)awidthshow
-499 90 gm
-0.07339 0. 32 0.00733 0.(sequence in the given group.  If a given operation is illegal in one sequence in a group \(i.e. alignment)awidthshow
-510 90 gm
-0.06820 0. 32 0.00682 0.(modification\) then it will not work in any of the sequences in that group.  Ungroup will remove the selected)awidthshow
-521 90 gm
--0.05171 0.(sequences from a given group.)ashow
-543 90 gm
-12 fz
-2 F /|______Times-Roman fnt
-(Compress)show
-555 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.01747 0.(Compress will remove gap characters from the selected sequences.  The user has the option of removing all)ashow
-566 90 gm
-0.34576 0. 32 0.03457 0.(gaps, or simply all columns containing nothing but gaps.  This is useful for minimizing the length of a)awidthshow
-577 90 gm
-0.05169 0.(subalignment.)ashow
-599 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.10784 0.(Reverse Sequence)ashow
-611 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.06991 0.(Reverses the selected sequences.  Alignment gaps are reversed as well.  The selected sequences will remain)ashow
-622 90 gm
--0.13101 0.(aligned after reversal.)ashow
-647 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.04180 0. 32 0.00418 0.( DNA/RNA menu)awidthshow
-671 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.16490 0.(Complement Sequence)ashow
-683 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.20431 0. 32 0.02043 0.(Converts DNA/RNA into its complement strand \(keeping full IUPAC ambiguity\).  This function has no)awidthshow
-694 90 gm
--0.01968 0.(effect on text, protein, or mask sequence.  Note that this function does not produce the reverse strand of DNA)ashow
-705 90 gm
--0.02952 0.(but merely converts A<->T and G<->C.  If the reverse strand is needed, remember to Complement and)ashow
-716 90 gm
--0.09683 0.(Reverse the sequence \(Edit menu\).)ashow
-F T cp
-%%Page: ? 10
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(10)show
-107 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.68984 0. 32 0.06898 0.(External Functions)awidthshow
-130 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02468 0.(See appendix C for a full description of functions supported in GDE 2.0  All external functions are described)ashow
-141 90 gm
-0.00610 0. 32 0.00061 0.(in the configuration file .GDEmenus.  Here is a brief description of some of the basic functions included.)awidthshow
-163 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.16563 0.(File menu)ashow
-186 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.07015 0.(New Sequence <meta n>)ashow
-186 198 gm
--0.05102 0.(Create a new sequence. Prompts for sequence type, and short name.)ashow
-208 90 gm
--0.03674 0.(Import foreign format)ashow
-219 90 gm
--0.03681 0.(Export foreign format)ashow
-219 198 gm
--0.08541 0.(Load and save sequences using Readseq by Don Gilbert \(see Appendix C\).)ashow
-241 90 gm
--0.01116 0.(Save Selection)ashow
-241 198 gm
--0.08074 0.(Save the currently selected sequences in a specified file.)ashow
-263 90 gm
-0.35308 0. 32 0.03530 0.(Print Selection)awidthshow
-263 198 gm
-0.01174 0. 32 0.00117 0.(Print the selected sequences to the chosen printer.  This function supports)awidthshow
-274 198 gm
-0.04150 0. 32 0.00415 0.(the Unix command enscript as well as lpr. The .GDEmenus file may need to)awidthshow
-285 198 gm
--0.00283 0.(be modified to add the names of local printers to the printer list.)ashow
-307 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.20724 0.(Edit menu)ashow
-330 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.25080 0.(sort...)ashow
-330 198 gm
--0.06867 0.(Sort the selected sequences by a primary and secondary key.  Pass the new order)ashow
-341 198 gm
--0.00726 0.(to a new GDE window.)ashow
-363 90 gm
--0.14492 0.(Extract)ashow
-363 198 gm
--0.07679 0.(Extract the selected sequences into a new window.)ashow
-385 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.24058 0.(DNA/RNA Menu)ashow
-397 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.14962 0.(Translate)ashow
-397 198 gm
--0.05361 0.(Translate the selected sequences from DNA/RNA to Amino acid.  The user can)ashow
-408 198 gm
--0.07470 0.(specify the desired reading frame, and the minimum open reading frame \(stop)ashow
-419 198 gm
--0.00601 0.(codon to stop codon\) to translate.  The user can also choose between single)ashow
-430 198 gm
--0.09318 0.(letter code and triple letter codes.)ashow
-452 90 gm
-0.55633 0. 32 0.05563 0.(Dot plot)awidthshow
-452 198 gm
--0.02882 0.(Display a dotplot identity matrix for the selected sequence\(s\).  If only one)ashow
-463 198 gm
-(sequence is selected, then the dotplot is a self comparison.  If two or more)show
-474 198 gm
--0.10966 0.(sequences are selected, then the first two sequences are compared.)ashow
-496 90 gm
-0.63247 0. 32 0.06324 0.(Clustal Align)awidthshow
-496 198 gm
-0.04074 0. 32 0.00407 0.(Align the selected sequences using the clustalv algorithm by Des Higgins.)awidthshow
-507 198 gm
--0.07983 0.(\(See Appendix C\))ashow
-529 90 gm
-0.29251 0. 32 0.02925 0.(Find All <meta f>)awidthshow
-529 198 gm
--0.04464 0.(Search and highlight the selected sequences for a given substring.  A specified)ashow
-540 198 gm
--0.02334 0.(percent of mismatching can also be allowed.)ashow
-562 90 gm
-0.15136 0. 32 0.01513 0.(Variable Positions)awidthshow
-562 198 gm
--0.06744 0.(The selected sequences are scored column by column for conservation.  The)ashow
-573 198 gm
-0.02929 0. 32 0.00292 0.(result is returned as a grey scale alignment color mask.  This can be useful)awidthshow
-584 198 gm
-0.41549 0. 32 0.04154 0.(in selecting PCR primers.)awidthshow
-606 90 gm
--0.09349 0.(Sequence Consensus)ashow
-606 198 gm
--0.02246 0.(Return the consensus for the selected sequences.  This can either be a majority)ashow
-617 198 gm
-0.17730 0. 32 0.01773 0.(consensus, or an ambiguity consensus using IUPAC coding.)awidthshow
-639 90 gm
--0.01284 0.(Distance Matrix )ashow
-639 198 gm
--0.07553 0.(Calculate a distance matrix for the selected sequences. \(See Appendix C\))ashow
-661 90 gm
-(MFOLD)show
-661 198 gm
--0.01577 0.(Fold the selected sequences using MFOLD by Michael Zuker.  The resulting)ashow
-672 198 gm
--0.08619 0.(structure is returned as a nested bracket \('[]'\) representation of the secondary)ashow
-683 198 gm
--0.05360 0.(structure.\(See appendix C.\))ashow
-705 90 gm
--0.13284 0.(Draw Secondary Structure)ashow
-705 198 gm
--0.07971 0.(Draw the selected sequence using the proposed secondary structure.  Both the)ashow
-716 198 gm
--0.11421 0.(secondary structure prediction, and the RNA sequence should be selected before)ashow
-F T cp
-%%Page: ? 11
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(11)show
-81 198 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.08117 0. 32 0.00811 0.(calling this function.  The drawing program is LoopTool. \(See Appendix C\))awidthshow
-103 90 gm
-0.39718 0. 32 0.03971 0.(Highlight Helix)awidthshow
-103 198 gm
--0.02478 0.(Show all violations to a proposed RNA secondary structure.  The secondary)ashow
-114 198 gm
--0.06376 0.(structure represented must be selected, as well as the aligned sequences to be)ashow
-125 198 gm
--0.06709 0.(tested.  The selected sequences will then be colored according to whether or not)ashow
-136 198 gm
--0.02209 0.(they support the proposed 2)ashow
-currentfont SwToSym
--0.02209 0.(\260)ashow
-setfont
--0.02209 0.( structure.  Standard Watson/Crick paring will be)ashow
-147 198 gm
-(colored dark blue, G-U paring will be colored light blue, mismatches will be)show
-158 198 gm
--0.03656 0.(colored gold, and pairng to gaps will be red.)ashow
-180 90 gm
--0.09217 0.(Blastn/BlastX)ashow
-180 198 gm
--0.06690 0.(Search the selected sequence \(select only one\) against a given database with the)ashow
-191 198 gm
-0.21972 0. 32 0.02197 0.(BLAST searching tool written by Altschul, Gish, Miller, Myers, and Lipman.)awidthshow
-202 198 gm
--0.05590 0.(Blastn searches DNA against DNA databases, blastx searches DNA against AA)ashow
-213 198 gm
--0.04621 0.(databases by translating the sequence in all six reading frames. \(See Appendix C\))ashow
-235 90 gm
-0.02897 0.(FastA)ashow
-235 198 gm
--0.06472 0.(Search the selected sequence \(select only one\) against a given database using the)ashow
-246 198 gm
-0.02075 0. 32 0.00207 0.(FASTA similarity search program written by Pearson and Lipman. \(See)awidthshow
-257 198 gm
--0.09335 0.(Appendix C\))ashow
-279 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.15008 0.(Protein Menu)ashow
-313 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.63247 0. 32 0.06324 0.(Clustal Align)awidthshow
-313 198 gm
--0.02090 0.(Align the selected amino acid sequences using the clustal algorithm. \(See)ashow
-324 198 gm
--0.09335 0.(Appendix C\))ashow
-346 90 gm
-0.21408 0. 32 0.02140 0.(Blastp, Tblastn, Blast3)awidthshow
-346 198 gm
--0.06690 0.(Search the selected sequence \(select only one\) against a given database with the)ashow
-357 198 gm
-0.21972 0. 32 0.02197 0.(BLAST searching tool written by Altschul, Gish, Miller, Myers, and Lipman.)awidthshow
-368 198 gm
--0.04742 0.(Blastp searches AA against AA databases, tblastn searches AA against DNA)ashow
-379 198 gm
--0.03672 0.(databases by translating the database in all six reading frames.  Blast3 finds)ashow
-390 198 gm
-0.00274 0. 32 0.00027 0.(three way alignments that are could not be found with only pairwise comparisons.)awidthshow
-401 198 gm
--0.07983 0.(\(See Appendix C\))ashow
-423 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.20037 0.(Sequence Management Menu)ashow
-446 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.07385 0. 32 0.00738 0.(Assemble contigs)awidthshow
-446 198 gm
-0.02410 0. 32 0.00241 0.(Assemble the selected sequences into contigs using the program CAP \(Contig)awidthshow
-457 198 gm
--0.03036 0.(Assemble Program\) written by Xiaoqiu Huang.  The resulting sequences are)ashow
-468 198 gm
--0.03370 0.(returned to the current GDE window, and they are grouped into contigs.  The)ashow
-479 198 gm
--0.05517 0.(user can then sort the sequences by group, and offset to produce an ordered list of)ashow
-490 198 gm
-0.02960 0. 32 0.00296 0.(the contigs. \(See Appendix C\))awidthshow
-512 90 gm
--0.02136 0.(Strategy view)ashow
-512 198 gm
-0.03570 0. 32 0.00357 0.(Pass out the selected sequences to StratView.  This program will display contigs)awidthshow
-523 198 gm
--0.01431 0.(in a greatly reduced line drawing.  This is very useful for large contigs.)ashow
-545 90 gm
-0.32684 0. 32 0.03268 0.(Restriction sites)awidthshow
-545 198 gm
--0.06761 0.(Search the selected sequences for the restriction enzymes specified in the given)ashow
-556 198 gm
--0.01243 0.(enzyme file.  The restriction sites are then colored by enzyme.)ashow
-578 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.07624 0.(Phylogeny menu)ashow
-602 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.07130 0.(DeSoete Tree fit)ashow
-602 198 gm
--0.00927 0.(Calculate a phylogenetic tree using a least squares fitting algorithm on a distance)ashow
-613 198 gm
--0.06059 0.(matrix calculated from the selected sequences.  The results can then be passed on)ashow
-624 198 gm
--0.01338 0.(to treetool for display and manipulation. \(See Appendix C\))ashow
-646 90 gm
-0.99151 0. 32 0.09915 0.(Phylip 3.4)awidthshow
-646 198 gm
-0.10299 0. 32 0.01029 0.(Pass the selected data to on of the treeing programs in Phylip, written by)awidthshow
-657 198 gm
-0.16418 0. 32 0.01641 0.(Joe Felsenstein.  The chosen phylip program is started in it's own window,)awidthshow
-668 198 gm
--0.12712 0.(with the selected sequences already loaded. \(See Appendix C\))ashow
-F T cp
-%%Page: ? 12
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(12)show
-106 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.70434 0. 32 0.07043 0.(Citation of work)awidthshow
-129 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.03417 0. 32 0.00341 0.(We ask that any published work using any of the external functions in GDE cite the appropriate authors.)awidthshow
-140 90 gm
--0.08705 0.(Please see Appendix C for references.)ashow
-187 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.42251 0. 32 0.04225 0.(Bug reports/extensions)awidthshow
-210 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03602 0.(Any bug reports, RFE's \(request for enhancement\), and useful extensions to the GDE should be forwarded by)ashow
-221 90 gm
-0.06652 0. 32 0.00665 0.(electronic mail to:)awidthshow
-243 90 gm
--0.12284 0.(smith@nucleus.harvard.edu)ashow
-265 90 gm
--0.01402 0.(Please include as much detail as possible in bug reports so that the bug can be reproduced.)ashow
-276 90 gm
--0.16358 0.(Correspondence should be addressed to:)ashow
-298 90 gm
-0.66253 0. 32 0.06625 0.(Steven Smith)awidthshow
-309 90 gm
-0.03417 0. 32 0.00341 0.(Director of Computation)awidthshow
-320 90 gm
--0.16851 0.(Harvard Genome Laboratory)ashow
-331 90 gm
-0.55831 0. 32 0.05583 0.(16. Divinity Ave.)awidthshow
-342 90 gm
--0.04499 0.(Cambridge, MA)ashow
-342 162 gm
-(02138)show
-433 90 gm
-14 fz
-2 F /|______Times-Roman fnt
--0.06921 0.(Acknowledgments)ashow
-456 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.01979 0.(I would like to thank the following people for their input and assistance and code used in the development of)ashow
-467 90 gm
-(the GDE:)show
-489 90 gm
-0.10726 0. 32 0.01072 0.(Carl Woese, Gary Olsen and Mike Maciukenas at University of Illinois Dept of Microbiology,  Ross)awidthshow
-500 90 gm
--0.02450 0.(Overbeek at Argonne National Laboratories,Walter Gilbert, Patrick Gillevet, Chunwei Wang and Susan)ashow
-511 90 gm
-0.02166 0. 32 0.00216 0.(Russo at the Harvard Genome Laboratory.  I would also like to personally thank the following people for)awidthshow
-522 90 gm
-0.02990 0. 32 0.00299 0.(their permission to include their software with this release of GDE.)awidthshow
-544 90 gm
-0.14419 0. 32 0.01441 0.(Des Higgins)awidthshow
-555 90 gm
--0.04928 0.(David Lipman and the group at NCBI)ashow
-566 90 gm
-0.03280 0. 32 0.00328 0.(William Pearson)awidthshow
-577 90 gm
-(Don Gilbert)show
-588 90 gm
--0.11433 0.(Xiaoqui Huang)ashow
-599 90 gm
-0.07690 0. 32 0.00769 0.(Joe Felsenstein)awidthshow
-610 90 gm
--0.09466 0.(Michael Zuker)ashow
-621 90 gm
--0.13116 0.(Geert DeSoete)ashow
-632 90 gm
--0.01974 0.(Michael Maciukenas and the group at the Ribosomal Database Project)ashow
-654 90 gm
-0.10925 0. 32 0.01092 0.(It is only by the generosity of these people that GDE has been successful.)awidthshow
-F T cp
-%%Page: ? 13
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(13)show
-95 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.57128 0. 32 0.05712 0.(Appendix A, File Formats)awidthshow
-122 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.03565 0.(The currently supported file formats include GDE data files, Genbank formatted files \(with type extensions\),)ashow
-133 90 gm
--0.01033 0.(a generic flat file format, and a color mask file.)ashow
-155 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.18190 0.(GDE format)ashow
-167 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.02778 0.(GDE format is a tagged field format used for storing all available information about a sequence.  The format)ashow
-178 90 gm
--0.03959 0.(matches very closely the GDE internal structures for sequence data.  The format consists of text records)ashow
-189 90 gm
--0.08013 0.(starting and ending with braces \('{}'\).  Between the open and close braces are several tagged field lines)ashow
-200 90 gm
--0.04377 0.(specifying different pieces of information about a given sequence.  The tag values can be wrapped with)ashow
-211 90 gm
--0.05966 0.(double quote characters \('""'\) as needed.  If quotes are not used, the first whitespace delimited string is taken)ashow
-222 90 gm
--0.03451 0.(as the value. The allowable fields are:)ashow
-244 90 gm
-({)show
-255 90 gm
--0.21841 0.(name)ashow
-255 162 gm
--0.09494 0.("Short name for sequence")ashow
-266 90 gm
--0.06198 0.(longname)ashow
-266 162 gm
--0.11402 0.("Long \(more descriptive\) name for sequence")ashow
-277 90 gm
--0.35173 0.(sequence-ID)ashow
-277 162 gm
--0.09922 0.("Unique ID number")ashow
-288 90 gm
--0.26521 0.(creation-date)ashow
-288 162 gm
-0.12008 0. 32 0.01200 0.("mm/dd/yy hh:mm:ss")awidthshow
-299 90 gm
--0.19244 0.(direction)ashow
-299 162 gm
--0.19648 0.([-1|1])ashow
-310 90 gm
--0.28077 0.(strandedness)ashow
-310 162 gm
--0.16368 0.([1|2])ashow
-321 90 gm
--0.07225 0.(type)ashow
-321 162 gm
--0.07638 0.([DNA|RNA||PROTEIN|TEXT|MASK])ashow
-332 90 gm
--0.15226 0.(offset)ashow
-332 162 gm
--0.03222 0.(\(-999999,999999\))ashow
-343 90 gm
--0.17175 0.(group-ID)ashow
-343 162 gm
--0.02587 0.(\(0,999\))ashow
-354 90 gm
--0.29151 0.(creator)ashow
-354 162 gm
--0.02342 0.("Author's name")ashow
-365 90 gm
--0.31198 0.(descrip)ashow
-365 162 gm
--0.12005 0.("Verbose description")ashow
-376 90 gm
--0.01441 0.(comments)ashow
-376 162 gm
--0.01306 0.("Lines of comments that can be fairly arbitrary)ashow
-387 90 gm
--0.03907 0.(text about a sequence.  Return characters are allowed, but no internal)ashow
-398 90 gm
--0.05203 0.(double quotes or brace characters.  Remember to close with a double)ashow
-409 90 gm
--0.25929 0.(quote")ashow
-420 90 gm
--0.37757 0.(sequence)ashow
-420 162 gm
--0.11505 0.("gctagctagctagctagctcttagctgtagtcgtagctgatgctagct)ashow
-431 90 gm
--0.13807 0.(gatgctagctagctagctagctgatcgatgctagctgatcgtagctgacg)ashow
-442 90 gm
--0.09281 0.(gactgatgctagctagctagctagctgtctagtgtcgtagtgcttattgc")ashow
-453 90 gm
-(})show
-475 90 gm
--0.03117 0.(Any fields that are not specified are assumed to be the default values.  Offsets can be negative as well as)ashow
-486 90 gm
--0.00729 0.(positive.  Genbank entries written out in this format will have all \("\) converted to \('\), and all \({}\) converted)ashow
-497 90 gm
--0.03678 0.(to \([]\) to avoid confusion in the parser.  Leading and trailing gaps are removed prior to writing each sequence.)ashow
-508 90 gm
--0.00801 0.(This format is deliberately verbose in order to be simple to duplicate.)ashow
-552 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.11645 0.(Genbank format:)ashow
-564 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.06373 0.(GDE can read a concatenated list of Genbank entries, and extract certain fields from such files.  The default)ashow
-575 90 gm
-(method for storing nucleic acid, amino acid, masking sequences or text is in Genbank format.  The following)show
-586 90 gm
--0.19308 0.(fields are recognized:)ashow
-608 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23880 0.(LOCUS:)ashow
-608 162 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.04878 0.(Short name for this sequence \(Maximum of 32 characters\))ashow
-0 -3 rm
-7 fz
-2 F /|______Times-Roman fnt
-(\240)show
-619 90 gm
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
--0.21890 0.(DEFINITION:)ashow
-619 162 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.06732 0.(Definition of sequence \(Maximum of 80 characters\))ashow
-630 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.22387 0.(ORGANISM:)ashow
-630 198 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-(Full name of organism \(Maximum of 80 characters\))show
-641 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.22743 0.(AUTHORS:)ashow
-641 198 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.04580 0.(Authors of this sequence \(Maximum of 80 characters\))ashow
-652 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.22111 0.(ACCESSION:)ashow
-652 162 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.06069 0.(ID Number for this sequence \(Maximum of 80 characters\))ashow
-663 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23217 0.(ORIGIN:)ashow
-663 162 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.16001 0.(Beginning of sequence data)ashow
-0 -3 rm
-7 fz
-2 F /|______Times-Roman fnt
-(\240)show
--4096 -4096 gm
--4095 -4095 0 gr
-lin
-6 25 lw
-691 90 gm
-691 233 lin
-25 6 lw
-1 1 lw
-704 90 gm
-0 gr
-T 1 setTxMode
-9 fz
-2 F /|______Times-Roman fnt
--0.03189 0.(\240 Required field)ashow
-F T cp
-%%Page: ? 14
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(14)show
-81 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.39801 0.(//)ashow
-81 198 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.22740 0.(End of sequence data)ashow
-0 -3 rm
-7 fz
-2 F /|______Times-Roman fnt
-(\240)show
-103 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.01617 0. 32 0.00161 0.(All other lines are retained as comments.  The LOCUS line also specifies what type of sequence follows.)awidthshow
-114 90 gm
-0.31143 0. 32 0.03114 0.(The form of this line is:)awidthshow
-133 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(LOCUS       )ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.26533 0.(name)ashow
-133 198 gm
--0.19900 0.(size)ashow
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
--0.29850 0.( bp)ashow
-133 234 gm
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.26533 0.(type)ashow
-133 270 gm
--0.26533 0.(date)ashow
-155 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.23757 0. 32 0.02375 0.(where )awidthshow
-2 fs
-{}mark T /Times-Italic /|______Times-Italic 0 rf
-2 F /|______Times-Italic fnt
-0.07641 0.(name)ashow
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-2 F /|______Times-Roman fnt
-0.19012 0. 32 0.01901 0.( is the Genbank Locus name, )awidthshow
-2 fs
-{}mark T /Times-Italic /|______Times-Italic 0 rf
-2 F /|______Times-Italic fnt
-0.16464 0. 32 0.01646 0.(size )awidthshow
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-2 F /|______Times-Roman fnt
-0.17791 0. 32 0.01779 0.(is total base count, )awidthshow
-2 fs
-{}mark T /Times-Italic /|______Times-Italic 0 rf
-2 F /|______Times-Italic fnt
-0.05877 0.(type)ashow
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-2 F /|______Times-Roman fnt
-0.21957 0. 32 0.02195 0.( is one of DNA, RNA, PROTEIN,)awidthshow
-166 90 gm
--0.03018 0.(MASK, or TEXT and )ashow
-2 fs
-{}mark T /Times-Italic /|______Times-Italic 0 rf
-2 F /|______Times-Italic fnt
--0.02607 0.(date)ashow
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-2 F /|______Times-Roman fnt
--0.02537 0.( is of the form dd-MON-yyyy.  In this way, the standard Genbank format is)ashow
-177 90 gm
--0.06455 0.(extended to store all text, mask and protein data.  The Genbank character set has also been extended in order)ashow
-188 90 gm
--0.04171 0.(to support these other data types.  Valid characters are:)ashow
-210 90 gm
--0.04614 0.(DNA/RNA:)ashow
-210 198 gm
--0.00355 0.(Full IUPAC coding as well as '-' and '~' characters for alignment)ashow
-221 198 gm
--0.10925 0.(gaps)ashow
-232 90 gm
-0.04852 0.(Protein:)ashow
-232 198 gm
--0.01260 0.(All valid single letter codes plus '-' and '~'.  Other ASCII characters)ashow
-243 198 gm
--0.04739 0.(may be inserted, however external functions may be confused by)ashow
-254 198 gm
--0.12287 0.(such characters.)ashow
-265 90 gm
-(Mask:)show
-265 198 gm
-0.01281 0. 32 0.00128 0.(All legal printable ASCII characters.  If used as a selection mask, all)awidthshow
-276 198 gm
-0.12207 0. 32 0.01220 0.(columns containing a '0' will be removed from any analysis.)awidthshow
-287 90 gm
--0.02584 0.(Text:)ashow
-287 198 gm
--0.05348 0.(All valid ASCII characters.)ashow
-309 90 gm
-0.05142 0. 32 0.00514 0.(Here is a valid Genbank entry for two E.coli tRNA's:)awidthshow
-328 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.20202 0.(LOCUS         ECOTRNT4      76 bp     RNA               28-JAN-1991)ashow
-336 90 gm
--0.20275 0.(DEFINITION  E. coli \(T4 infected\) vulnerable tRNA \(A\).)ashow
-344 90 gm
--0.20637 0.(  ORGANISM  Escherichia coli)ashow
-352 90 gm
--0.20315 0.(   AUTHORS  Amitsur,M., Levitz,R. and Kaufmann,G.)ashow
-360 90 gm
--0.20362 0.(FEATURES       From  To/Span     Description)ashow
-368 90 gm
--0.20298 0.(    tRNA          1       76     vulnerable tRNA\(A\))ashow
-376 90 gm
--0.21559 0.(BASE COUNT  ?)ashow
-384 90 gm
--0.23880 0.(ORIGIN)ashow
-392 90 gm
--0.20169 0.(        1 GGGUCGUUAG CUCAGUUGGU AGAGCAGUUG ACUUUUAAUC AAUUGGNCGC AGGUUCGAAU)ashow
-400 90 gm
--0.20666 0.(       61 CCUGCACGAC CCACCA)ashow
-408 90 gm
--0.39801 0.(//)ashow
-416 90 gm
--0.20202 0.(LOCUS          ECOTRQ1      75 bp     RNA               28-JAN-1991)ashow
-424 90 gm
--0.20587 0.(DEFINITION  E.coli Gln-tRNA-1.)ashow
-432 90 gm
--0.20637 0.(  ORGANISM  Escherichia coli)ashow
-440 90 gm
--0.20503 0.(   AUTHORS  Yaniv,M. and Folk,W.R.)ashow
-448 90 gm
--0.20166 0.(SOURCE      -REFERENCE   [1]  JOURNAL   J. Biol. Chem. 250, 3243-3253 \(1975\))ashow
-456 90 gm
--0.20362 0.(FEATURES       From  To/Span     Description)ashow
-464 90 gm
--0.20269 0.(    tRNA          1       75     Gln-tRNA-1 \(NAR: 0510\))ashow
-472 90 gm
--0.20231 0.(    refnumbr      1        1     sequence not numbered in [1])ashow
-480 90 gm
--0.21559 0.(BASE COUNT  ?)ashow
-488 90 gm
--0.23880 0.(ORIGIN)ashow
-496 90 gm
--0.20169 0.(        1 UGGGGUAUCG CCAAGCGGUA AGGCACCGGU UUUUGAUACC GGCAUUCCCU GGUUCGAAUC)ashow
-504 90 gm
--0.20697 0.(       61 CAGGUACCCC AGCCA)ashow
-512 90 gm
--0.39801 0.(//)ashow
-545 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-12 fz
-2 F /|______Times-Roman fnt
--0.18539 0.(Flat file format:)ashow
-557 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.11169 0. 32 0.01116 0.(This is a simplified format for importing sequence data, and passing it out to analysis functions.  Very little)awidthshow
-568 90 gm
-0.02944 0. 32 0.00294 0.(information is actually retained in this format, and should be used carefully so as not to lose attribute)awidthshow
-579 90 gm
-0.03372 0. 32 0.00337 0.(information.  It is defined as follow:)awidthshow
-598 90 gm
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-7 fz
-2 F /|______Courier-Oblique fnt
--0.20729 0.(type_character short_name)ashow
-606 90 gm
--0.21559 0.(sequence_data)ashow
-614 90 gm
--0.21559 0.(sequence_data)ashow
-622 90 gm
--0.21559 0.(sequence_data)ashow
-630 90 gm
--0.29850 0.(...)ashow
-652 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.02508 0.(The type character is # for DNA/RNA, % for protein sequence, @ for mask sequence, and " for text.  The)ashow
-663 90 gm
-0.07781 0. 32 0.00778 0.(short name is the same as the LOCUS line in Genbank.  This is followed by lines of sequence, each ending)awidthshow
-674 90 gm
--0.03877 0.(with a return character.These lines are read until the next type character is encountered, or until the end of the)ashow
-685 90 gm
--0.01963 0.(file is reached.  Care should be taken in using this format with text as space characters are stripped)ashow
--4096 -4096 gm
--4095 -4095 0 gr
-lin
-6 25 lw
-703 90 gm
-703 233 lin
-25 6 lw
-1 1 lw
-F T cp
-%%Page: ? 15
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(15)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.03921 0. 32 0.00392 0.(automatically.  As of release 2.0, flat file format allows for an optional offset to be specified in parentheses)awidthshow
-92 90 gm
--0.07716 0.(after the sequence name.  An offset represents how many leading gap characters should be placed before the)ashow
-103 90 gm
-0.07568 0. 32 0.00756 0.(start of a sequence.  If this offset does not exist, then it is defined to be 0.)awidthshow
-125 90 gm
-0.13809 0. 32 0.01380 0.(Here is a sample flat file for two Ecoli tRNA's:)awidthshow
-144 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.22387 0.(#ECOTRNT4)ashow
-152 90 gm
--0.20237 0.(GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGNCGCAGGUUCGAAU)ashow
-160 90 gm
--0.21226 0.(CCUGCACGACCCACCA)ashow
-168 90 gm
--0.22743 0.(#ECOTRQ1)ashow
-176 90 gm
--0.20237 0.(UGGGGUAUCGCCAAGCGGUAAGGCACCGGUUUUUGAUACCGGCAUUCCCUGGUUCGAAUC)ashow
-184 90 gm
--0.21322 0.(CAGGUACCCCAGCCA)ashow
-217 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-12 fz
-2 F /|______Times-Roman fnt
--0.09919 0.(Color mask:)ashow
-229 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.10299 0. 32 0.01029 0.(The format for a color mask has been kept simple to make implementation of color functions easy.  The)awidthshow
-240 90 gm
-0.05355 0. 32 0.00535 0.(format optionally defines which sequence to color, whether or not to color alignment gaps in the existing)awidthshow
-251 90 gm
-0.04089 0. 32 0.00408 0.(sequence, and how long the following mask will be.  It is then followed by a list of decimal color codes)awidthshow
-262 90 gm
--0.01760 0.(\(range 0 to 15\) for each position in the sequence.  There are four keywords used in the color mask file.)ashow
-273 90 gm
--0.12745 0.(Those keywords are:)ashow
-295 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(name:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.22111 0.(short name)ashow
-295 234 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.09985 0.(If short name matches a currently loaded sequence,)ashow
-306 234 gm
-0.16754 0. 32 0.01675 0.(then impose this color mask on that sequence.  If this)awidthshow
-317 234 gm
-0.04577 0. 32 0.00457 0.(line is omitted, then color all sequences this color, and the color)awidthshow
-328 234 gm
-0.10223 0. 32 0.01022 0.(mask is expected to start at the leftmost column on the screen.)awidthshow
-350 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(length:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.23880 0.(length)ashow
-350 234 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.40191 0. 32 0.04019 0.(The following list in length long)awidthshow
-372 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23217 0.(nodash:)ashow
-372 234 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.00579 0. 32 0.00057 0.(Skip over dash characters when imposing this color mask)awidthshow
-383 234 gm
--0.03414 0.(on the named sequence.  This allows an unaligned color)ashow
-394 234 gm
--0.09637 0.(mask to be placed over aligned sequence.)ashow
-416 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23880 0.(start:)ashow
-416 234 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.02685 0. 32 0.00268 0.(Begin reading the color mask on the next line.)awidthshow
-438 90 gm
-0.04302 0. 32 0.00430 0.(Here is a sample color mask file:)awidthshow
-457 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.21070 0.(name:test_sequence)ashow
-465 90 gm
--0.22387 0.(length:10)ashow
-473 90 gm
--0.23217 0.(nodash:)ashow
-481 90 gm
--0.23880 0.(start:)ashow
-489 90 gm
-(3)show
-497 90 gm
-(3)show
-505 90 gm
-(3)show
-513 90 gm
-(6)show
-521 90 gm
-(5)show
-529 90 gm
-(3)show
-537 90 gm
-(3)show
-545 90 gm
-(3)show
-553 90 gm
-(2)show
-561 90 gm
-(7)show
-580 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.00993 0.(The colors in the default color lookup table are:)ashow
-591 90 gm
-(0)show
-591 126 gm
--0.10839 0.(White)ashow
-591 270 gm
-(8)show
-591 306 gm
--0.33126 0.(Black)ashow
-602 90 gm
-(1)show
-602 126 gm
--0.08668 0.(Yellow)ashow
-602 234 gm
-(9)show
-602 270 gm
--0.09704 0.(Grey 1)ashow
-613 90 gm
-(2)show
-613 126 gm
-(Violet)show
-613 270 gm
-(10)show
-613 306 gm
--0.09704 0.(Grey 2)ashow
-624 90 gm
-(3)show
-624 126 gm
--0.55415 0.(Red)ashow
-624 270 gm
-(11)show
-624 306 gm
--0.09704 0.(Grey 3)ashow
-635 90 gm
-(4)show
-635 126 gm
--0.55255 0.(Aqua)ashow
-635 270 gm
-(12)show
-635 306 gm
--0.09704 0.(Grey 4)ashow
-646 90 gm
-(5)show
-646 126 gm
--0.11416 0.(Lime Green)ashow
-646 270 gm
-(13)show
-646 306 gm
--0.09704 0.(Grey 5)ashow
-657 90 gm
-(6)show
-657 126 gm
--0.29557 0.(Blue)ashow
-657 270 gm
-(14)show
-657 306 gm
--0.09704 0.(Grey 6)ashow
-668 90 gm
-(7)show
-668 126 gm
--0.02070 0.(Purple)ashow
-668 270 gm
-(15)show
-668 306 gm
--0.10839 0.(White)ashow
-F T cp
-%%Page: ? 16
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(16)show
-84 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.21636 0. 32 0.02163 0.(Appendix B, Adding Functions)awidthshow
-107 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.04040 0.(The GDE uses a menu description language to define what external programs it can call, and what parameters)ashow
-118 90 gm
-0.08483 0. 32 0.00848 0.(and data to pass to each function.  This language allows users to customize their own environment to suite)awidthshow
-129 90 gm
--0.14483 0.(individual needs.)ashow
-151 90 gm
--0.02262 0.(The following is how the GDE handles external programs when selected from a menu:)ashow
-0 0 gm
-(nc 164 126 255 369 6 rc)kp
-64 gr
-164 211 202 277 14.5 14.5 4 rr
-0 gr
-164.5 211.5 201.5 276.5 14.5 14.5 0 rr
-64 gr
-164 126 202 192 14.5 14.5 4 rr
-0 gr
-164.5 126.5 201.5 191.5 14.5 14.5 0 rr
-64 gr
-164 300 202 366 14.5 14.5 4 rr
-0 gr
-164.5 300.5 201.5 365.5 14.5 14.5 0 rr
-183 192 gm
-(nc 164 126 255 208 6 rc)kp
-183 211 lin
-(nc 164 126 255 369 6 rc)kp
-177 205 190 218 165 195 4 ar
-183 277 gm
-(nc 164 126 255 296 6 rc)kp
-183 300 lin
-(nc 164 126 255 369 6 rc)kp
-177 293 190 307 165 195 4 ar
-145 385 91 243 th
-177 133 gm
-0 gr
-T 1 setTxMode
-12 fz
-2 F /|______Times-Roman fnt
--0.17835 0.(Display dialog)ashow
-185 133 gm
--0.07539 0.(box presenting)ashow
-192 133 gm
-0.30838 0. 32 0.03083 0.(user options.)awidthshow
-177 215 gm
--0.19335 0.(Write out selected)ashow
-185 215 gm
--0.13066 0.(data \(if any\) to)ashow
-192 215 gm
--0.06405 0.(temporary files.)ashow
-177 303 gm
--0.20286 0.(Call external )ashow
-185 303 gm
-(function, passing)show
-192 303 gm
--0.10202 0.(parameters and data.)ashow
-tu
-64 gr
-214 300 255 366 4 rc
-0 gr
-214.5 300.5 254.5 365.5 0 rc
-202 331 gm
-(nc 164 126 211 369 6 rc)kp
-214 331 lin
-(nc 164 126 255 369 6 rc)kp
-208 325 221 338 255 285 4 ar
-ts
-224 307 gm
-0 gr
-T 1 setTxMode
--0.15270 0.(External program)ashow
-232 307 gm
-0.09719 0. 32 0.00971 0.(runs analysis, and)awidthshow
-239 307 gm
--0.06079 0.(writes results to)ashow
-247 307 gm
--0.06405 0.(temporary files.)ashow
-tu
-64 gr
-217 211 255 277 14.5 14.5 4 rr
-0 gr
-217.5 211.5 254.5 276.5 14.5 14.5 0 rr
-236 300 gm
-(nc 164 281 255 369 6 rc)kp
-236 277 lin
-(nc 164 126 255 369 6 rc)kp
-230 271 243 284 345 375 4 ar
-ts
-227 218 gm
-0 gr
-T 1 setTxMode
--0.08067 0.(GDE reads results)ashow
-235 218 gm
--0.11495 0.(of temporary files)ashow
-242 218 gm
-0.20019 0. 32 0.02001 0.(\(if any\).)awidthshow
-tu
-64 gr
-217 126 255 192 14.5 14.5 4 rr
-0 gr
-217.5 126.5 254.5 191.5 14.5 14.5 0 rr
-236 211 gm
-(nc 164 195 255 369 6 rc)kp
-236 192 lin
-(nc 164 126 255 369 6 rc)kp
-230 186 243 199 345 375 4 ar
-ts
-227 133 gm
-0 gr
-T 1 setTxMode
--0.13632 0.(GDE cleans up)ashow
-235 133 gm
--0.06405 0.(temporary files,)ashow
-242 133 gm
--0.04287 0.(and displays new)ashow
-250 133 gm
-(data.)show
-tu
-275 90 gm
-(nc 31 30 761 582 6 rc)kp
-10 fz
-2 F /|______Times-Roman fnt
-0.03387 0. 32 0.00338 0.(Each step in this process is described in a file .GDEmenus in the user's current or home)awidthshow
-286 90 gm
--0.17651 0.(directory.)ashow
-308 90 gm
--0.02418 0.(The language used in this file describes three phases to an external function call.  The first phase describes)ashow
-319 90 gm
-0.12283 0. 32 0.01228 0.(the menu item as it will appear, and the Unix command line that is actually run when it is selected.  The)awidthshow
-330 90 gm
--0.06280 0.(second phase describes how to prompt for the parameters needed by the function.  The third phase describes)ashow
-341 90 gm
--0.05538 0.(what data needs to be passed as input to the external function, and what data \(if any\) needs to be read back)ashow
-352 90 gm
-0.58975 0. 32 0.05897 0.(from its output.)awidthshow
-374 90 gm
--0.01350 0.(The form of the language is a simple keyword/value list delimited by the colon \(:\) character.  The language)ashow
-385 90 gm
-0.13610 0. 32 0.01361 0.(retains old values until new ones are set.  For example, setting the menu name is done once for all items in)awidthshow
-396 90 gm
-0.02822 0. 32 0.00282 0.(that menu, and is only reset when the next menu is reached.)awidthshow
-418 90 gm
--0.09211 0.(The keywords for phase one are:)ashow
-440 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(menu:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.22387 0.(menu name)ashow
-440 306 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.06471 0.(Name of current menu)ashow
-451 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(item:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.22387 0.(item name)ashow
-451 306 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.02093 0.(Name of current menu item)ashow
-462 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(itemmeta:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.22743 0.(meta_key)ashow
-462 306 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.12283 0.(Meta key equivalence \(quick keys\))ashow
-473 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(itemhelp:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.22387 0.(help_file)ashow
-473 306 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.15548 0. 32 0.01554 0.(Help file \(either full path, or in)awidthshow
-484 306 gm
--0.09056 0.(GDE_HELP_DIR\))ashow
-492 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(itemmethod:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21710 0.(Unix command)ashow
-514 90 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.14251 0. 32 0.01425 0.(The item method command is a bit more involved, it is the Unix command that will actually run the)awidthshow
-525 90 gm
-0.02655 0. 32 0.00265 0.(external program intended.  It is one line long, and can be up to 256 characters in length.  It can have)awidthshow
-536 90 gm
--0.02996 0.(embedded variable names \(starting with a '$'\) that will be replaced with appropriate values later on.  It can)ashow
-547 90 gm
--0.00277 0.(consist of multiple Unix commands separated by semi-colons \(;\), and may contain shell scripts and)ashow
-558 90 gm
-0.00350 0. 32 0.00035 0.(background processes as well as simple command names.  Examples will be given later.)awidthshow
-580 90 gm
--0.07740 0.(The keywords for phase two are:)ashow
-602 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(arg:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.20848 0.(argument_variable_name)ashow
-602 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.07934 0. 32 0.00793 0.(Name of this variable.  It will appear)awidthshow
-613 342 gm
-0.09628 0. 32 0.00962 0.(in the itemmethod: line with a dollar)awidthshow
-624 342 gm
-0.35354 0. 32 0.03535 0.(sign \($\) in front of it.)awidthshow
-635 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argtype:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.20503 0.(slider,chooser,choice_menu or text)ashow
-635 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.02027 0.(The type of graphic object)ashow
-646 342 gm
--0.00474 0.(representing this argument.)ashow
-668 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(arglabel:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21144 0.(descriptive label)ashow
-668 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.07995 0. 32 0.00799 0.(A short description of what this)awidthshow
-679 342 gm
--0.09936 0.(argument represents)ashow
-701 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argmin:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.20805 0.(minimum_value \(integer\))ashow
-701 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.11270 0.(Used for sliders.)ashow
-723 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argmax:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.20805 0.(maximum_value \(integer\))ashow
-723 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.11270 0.(Used for sliders.)ashow
-F T cp
-%%Page: ? 17
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(17)show
-92 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argvalue:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.20805 0.(default_value \(integer\))ashow
-92 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.00714 0.(It is the numeric value associated with)ashow
-103 342 gm
--0.05737 0.(sliders or the default choice in)ashow
-114 342 gm
--0.06477 0.(choosers and choice_menus \(the first)ashow
-125 342 gm
-0.10726 0. 32 0.01072 0.(choice is 0, the second is 1 etc.\))awidthshow
-147 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argtext:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21559 0.(default value)ashow
-147 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.07046 0.(Used for text fields.)ashow
-169 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(argchoice:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.19900 0.(displayed value)ashow
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
--0.19900 0.(:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21710 0.(passed value)ashow
-169 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.15618 0.(Used for choosers and)ashow
-180 342 gm
-0.10101 0. 32 0.01010 0.(choice_menus.  The first value is)awidthshow
-191 342 gm
--0.12577 0.(displayed on screen, and the second)ashow
-202 342 gm
--0.00753 0.(value is passed to the itemmethod)ashow
-213 342 gm
-0.12620 0.(line.)ashow
-235 90 gm
--0.06112 0.(The keywords for phase three are as follows:)ashow
-257 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(in:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.19900 0.(input_file)ashow
-0 fs
-{}mark T /Courier /|______Courier 0 rf
-2 F /|______Courier fnt
-( )show
-257 342 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.07873 0. 32 0.00787 0.(GDE will replace this name with a)awidthshow
-268 342 gm
--0.12794 0.(randomly generated temporary file)ashow
-279 342 gm
-(name. It will then write the selected)show
-290 342 gm
-0.24902 0. 32 0.02490 0.(data out to this file.)awidthshow
-312 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(informat:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21890 0.(file_format)ashow
-312 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.14724 0. 32 0.01472 0.(Write data to this file for input to)awidthshow
-323 342 gm
-0.33538 0. 32 0.03353 0.(this function.  Currently support)awidthshow
-334 342 gm
--0.05738 0.(values are Genbank, and flat.)ashow
-345 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23217 0.(inmask:)ashow
-345 342 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.05563 0.(This data can be controlled by a)ashow
-356 342 gm
-0.14770 0. 32 0.01477 0.(selection mask.)awidthshow
-378 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.23217 0.(insave:)ashow
-378 342 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.08697 0. 32 0.00869 0.(Do not remove this file after running)awidthshow
-389 342 gm
-0.19424 0. 32 0.01942 0.(the external function.  This is useful)awidthshow
-400 342 gm
-0.01831 0. 32 0.00183 0.(for functions put in the background.)awidthshow
-422 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(out:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21890 0.(output_file)ashow
-422 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.07873 0. 32 0.00787 0.(GDE will replace this name with a)awidthshow
-433 342 gm
--0.12794 0.(randomly generated temporary file)ashow
-444 342 gm
-0.21469 0. 32 0.02146 0.(name.  It is up to the external function)awidthshow
-455 342 gm
-0.36849 0. 32 0.03684 0.(to fill this file with any results that)awidthshow
-466 342 gm
-0.03570 0. 32 0.00357 0.(might be read back into the GDE.)awidthshow
-488 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.19900 0.(outformat:)ashow
-2 fs
-{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
-2 F /|______Courier-Oblique fnt
--0.21890 0.(file_format)ashow
-488 342 gm
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.18402 0. 32 0.01840 0.(The data in the output file will be in)awidthshow
-499 342 gm
-0.29846 0. 32 0.02984 0.(this format.  Currently support)awidthshow
-510 342 gm
--0.05863 0.(values are colormask, Genbank, and)ashow
-521 342 gm
-0.04431 0.(flat.)ashow
-543 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.22743 0.(outsave:)ashow
-543 342 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.01464 0.(Do not remove this file after reading.)ashow
-554 342 gm
-0.03158 0. 32 0.00315 0.(This is useful for background tasks.)awidthshow
-576 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.21559 0.(outoverwrite:)ashow
-576 342 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.06021 0.(Overwrite existing sequences in the current)ashow
-587 342 gm
--0.00816 0.(GDE window.  Currently supported with)ashow
-598 342 gm
--0.03097 0.("gde" format only.)ashow
-642 90 gm
-0.11749 0. 32 0.01174 0.(Here is a sample dialog box, and it's entry in the .GDEmenus file:)awidthshow
-F T cp
-%%Page: ? 18
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(18)show
-454 408 241 216 th
-147 170 gm
-tu
-(nc 143 169 312 327 6 rc)kp
-ts
-{}mark T /Courier /|______Courier 0 rf
-8.33332 fz
-2 F /|______Courier fnt
-( )show
-165 170 gm
-(menu:Test function)show
-177 170 gm
-(item:All capitals)show
-182 170 gm
-(itemmethod:\(tr '[a-z]' '[A-Z]' < INPUT_FILE > )show
-188 170 gm
-(INPUT_FILE.tmp ; mv INPUT_FILE.tmp $SAVE_FILE_NAME ; gde )show
-194 170 gm
-($SAVE_FILE_NAME -Wx $SIZE ; rm INPUT_FILE\) &)show
-206 170 gm
-(arg:SAVE_FILE_NAME)show
-212 170 gm
-(argtype:text)show
-217 170 gm
-(arglabel:Save converted data as?)show
-223 170 gm
-(argtext:CAPS)show
-235 170 gm
-(arg:SIZE)show
-241 170 gm
-(arglabel:Text size?)show
-247 170 gm
-(argtype:chooser)show
-252 170 gm
-(argvalue:1)show
-258 170 gm
-(argchoice:Small:small)show
-264 170 gm
-(argchoice:Medium:medium)show
-270 170 gm
-(argchoice:Large:large)show
-276 170 gm
-(argchoice:Extra Large:extra_large)show
-288 170 gm
-(in:INPUT_FILE)show
-293 170 gm
-(informat:flat)show
-299 170 gm
-(insave:)show
-tu
-305 170 gm
-(nc 72 162 313 378 6 rc)kp
-64 gr
-73 166 142 355 1 rc
-0 gr
-73.5 166.5 141.5 354.5 0 rc
-64 gr
-79 174 89 193 12.5 12.5 1 rr
-0 gr
-79.5 174.5 88.5 192.5 12.5 12.5 0 rr
-64 gr
-77 172 137 352 1 rc
-0 gr
-T 180 31.07141 172 77 44 341 58 T 1 db
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-119 301 gm
-119 274 lin
-119 240 gm
-119 214 lin
-130 241 gm
-130 276 lin
-119 301 gm
-119 345 lin
-130 215 gm
-119 215 lin
-78.5 173.5 88.5 192.5 12.5 12.5 0 rr
-78.5 197.5 88.5 228.5 12.5 12.5 0 rr
-119 275 gm
-130 275 lin
-130 241 lin
-200.5 163.5 224.5 263.5 13.5 13.5 0 rr
-pr
-100 268 pl
-98 275 pl
-100 275 pl
-102 275 pl
-100 268 pl
-1 ep
-100 377 gm
-100 275 0 gr
-lin
-229.5 163.5 276.5 263.5 13.5 13.5 0 rr
-0 0 pen
-248 325 gm
-248 325 lin
-nc ct 39 0 put
-1 1 pen
-248 263 gm
-bp
-248 325 F qi
-248 325 qc
-248 363 qc
-248 363 qc
-124 363 qc
-124 363 F qq
-ef
-9 ec
-(nc 72 162 313 378 6 rc)kp
-248 363 gm
-pr
-124 349 pl
-122 356 pl
-124 356 pl
-126 356 pl
-124 349 pl
-1 ep
-124 363 gm
-124 356 0 gr
-lin
-100 377 gm
-215 377 lin
-215 263 gm
-215 377 lin
-322 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.02491 0.(Using the default parameters given in the dialog box, the executed Unix command line would be:)ashow
-341 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.20088 0.(\(tr '[a-z]' '[A-Z]' < .gde_001 >.gde_001.tmp ; mv .gde_001.tmp CAPS ; gde CAPS -Wx medium ; rm .gde_001 \) &)ashow
-363 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.06463 0.(where )ashow
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.06048 0.(.gde_001)ashow
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.05946 0.( is the name of the temporary file generated by the GDE which contains the selected sequences)ashow
-374 90 gm
-0.09124 0. 32 0.00912 0.(in flat file format.  Since the GDE runs this command in the background \('&' at the end\) it is necessary to)awidthshow
-385 90 gm
-(specify the )show
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
-(insave: )show
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
--0.00428 0.(line, and to remove all temporary files manually.  There is no output file specific because)ashow
-396 90 gm
--0.02909 0.(the data is not loaded back into the current GDE window, but rather a new GDE window is opened on the)ashow
-407 90 gm
--0.01303 0.(file.  A simpler command that reloads the data after conversion might be:)ashow
-426 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.21559 0.(item:All caps)ashow
-434 90 gm
--0.20352 0.(itemmethod:tr '[a-z]' '[A-Z]' <INPUT > OUTPUT)ashow
-450 90 gm
--0.22743 0.(in:INPUT)ashow
-458 90 gm
--0.21559 0.(informat:flat)ashow
-474 90 gm
--0.22111 0.(out:OUTPUT)ashow
-482 90 gm
--0.21430 0.(outformat:flat)ashow
-501 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.06103 0. 32 0.00610 0.(In this example, no arguments are specified, and so no dialog box will appear.  The command is not run in)awidthshow
-512 90 gm
--0.03242 0.(the background, so the GDE can clean up after itself automatically.  The converted sequence is automatically)ashow
-523 90 gm
--0.07383 0.(loaded back into the current GDE window.)ashow
-545 90 gm
-0.02014 0. 32 0.00201 0.(In general, the easiest type of program to integrate into the GDE is a program completely driven from a)awidthshow
-556 90 gm
--0.00051 0.(Unix command line.  Interactive programs can be tied in \(MFOLD for example\), however shell scripts must)ashow
-567 90 gm
--0.01737 0.(be used to drive the parameter entry for these programs.  Programs of the form:)ashow
-586 90 gm
-{}mark T /Courier /|______Courier 0 rf
-7 fz
-2 F /|______Courier fnt
--0.20149 0.(program_name -a1 argument1 -a2 arguement2 -f inputfile -er errorfile > outputfile)ashow
-608 90 gm
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-10 fz
-2 F /|______Times-Roman fnt
-0.06240 0. 32 0.00624 0.(can be specified in the .GDEmenus file directly. As this is the general form of most one Unix commands,)awidthshow
-619 90 gm
-0.06774 0. 32 0.00677 0.(these tend to be simpler to implement under the GDE.)awidthshow
-641 90 gm
-0.07995 0. 32 0.00799 0.(As functions grow in complexity, they may begin to need a user interface of their own.  In these cases, the)awidthshow
-652 90 gm
--0.01388 0.(command line calling arguments are still necessary in order to allow the GDE to hand them the appropriate)ashow
-663 90 gm
--0.02767 0.(data, and possible retrieve results after some external manipulation.)ashow
-F T cp
-%%Page: ? 19
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(19)show
-84 90 gm
-14 fz
-2 F /|______Times-Roman fnt
-0.49774 0. 32 0.04977 0.(Appendix C, External functions)awidthshow
-107 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.08163 0. 32 0.00816 0.(ClustalV - Cluster multiple sequence alignment)awidthshow
-129 90 gm
-0.30380 0. 32 0.03038 0.(Author: Des Higgins.)awidthshow
-151 90 gm
--0.25508 0.(Reference:)ashow
-151 162 gm
-0.14328 0. 32 0.01432 0.(Higgins,D.G. Bleasby,A.J. and Fuchs,R. \(1991\) CLUSTAL V: improved software)awidthshow
-162 162 gm
-0.13442 0. 32 0.01344 0.(for multiple sequence alignment.  ms. submitted to CABIOS)awidthshow
-183 90 gm
--0.11924 0.(Parameters:)ashow
-194 162 gm
--0.07839 0.(k-tuple pairwise search)ashow
-194 270 gm
--0.07196 0.(Word size for pairwise comparisons)ashow
-205 162 gm
--0.14807 0.(Window size)ashow
-205 270 gm
-0.07278 0. 32 0.00727 0.(Smaller values give faster alignments,)awidthshow
-216 270 gm
--0.03422 0.(larger values are more sensitive.)ashow
-227 162 gm
--0.05999 0.(Transitions weighted)ashow
-227 270 gm
-0.19729 0. 32 0.01972 0.(Can weight transitions twice as high as)awidthshow
-238 270 gm
--0.01446 0.(transversions \(DNA only\).)ashow
-249 162 gm
--0.04051 0.(Fixed gap penalty)ashow
-249 270 gm
-0.06027 0. 32 0.00602 0.(Gap insertion penalty, lower value, more gaps)awidthshow
-260 162 gm
-0.20385 0. 32 0.02038 0.(Floating gap penalty)awidthshow
-260 270 gm
-0.02777 0. 32 0.00277 0.(Gap extension penalty, lower value, longer gaps)awidthshow
-304 90 gm
-0.11117 0.(Comments:)ashow
-315 162 gm
--0.01083 0.(ClustalV is a directed multiple sequence alignment algorithm that)ashow
-326 162 gm
-0.06652 0. 32 0.00665 0.(aligns a set of sequences based on their level of similarity.  It first)awidthshow
-337 162 gm
-0.05584 0. 32 0.00558 0.(uses a Lipman Peasron pairwise similarity scoring to find "clusters")awidthshow
-348 162 gm
--0.06562 0.(of similar sequences, and pre-aligns those sequences.  It then adds)ashow
-359 162 gm
-0.03463 0. 32 0.00346 0.(other sequences to the alignment in the order of their similarity so as)awidthshow
-370 162 gm
--0.02696 0.(to produce the cleanest alignment.)ashow
-392 162 gm
-0.09170 0. 32 0.00917 0.(Warning:  ClustalV only uses unambiguous character codes.  It will also)awidthshow
-403 162 gm
-0.04348 0. 32 0.00434 0.(convert all sequences to upper case in the process of aligning.  Clustal)awidthshow
-414 162 gm
-0.04180 0. 32 0.00418 0.(does not pass back comments, author etc.  Be sure to keep copies of your)awidthshow
-425 162 gm
-0.15106 0. 32 0.01510 0.(sequences if you do not wish to lose this information.)awidthshow
-F T cp
-%%Page: ? 20
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(20)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.08074 0.(MFOLD - RNA secondary prediction)ashow
-103 90 gm
--0.03694 0.(Author: Michael Zuker)ashow
-125 90 gm
--0.17959 0.(Reference: )ashow
-125 162 gm
-0.13900 0. 32 0.01390 0.(M. Zuker)awidthshow
-136 162 gm
-0.27359 0. 32 0.02735 0.(On Finding All Suboptimal Foldings of an RNA Molecule.)awidthshow
-147 162 gm
-0.16525 0. 32 0.01652 0.(Science, 244, 48-52, \(1989\))awidthshow
-169 162 gm
-0.12847 0. 32 0.01284 0.(J. A. Jaeger, D. H. Turner and M. Zuker)awidthshow
-180 162 gm
--0.06132 0.(Improved Predictions of Secondary Structures for RNA.)ashow
-191 162 gm
-0.25482 0. 32 0.02548 0.(Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, \(1989\))awidthshow
-213 162 gm
-0.12847 0. 32 0.01284 0.(J. A. Jaeger, D. H. Turner and M. Zuker)awidthshow
-224 162 gm
--0.01690 0.(Predicting Optimal and Suboptimal Secondary Structure for RNA.)ashow
-235 162 gm
-0.13473 0. 32 0.01347 0.(in "Molecular Evolution: Computer Analysis of Protein and)awidthshow
-246 162 gm
-(Nucleic Acid Sequences", R. F. Doolittle ed.)show
-257 162 gm
-0.18035 0. 32 0.01803 0.(Methods in Enzymology, 183, 281-306 \(1989\))awidthshow
-279 90 gm
--0.11924 0.(Parameters:)ashow
-290 162 gm
--0.11352 0.(Linear/circular RNA fold)ashow
-301 162 gm
-0.25527 0. 32 0.02552 0.(ct File to save results)awidthshow
-323 90 gm
-0.11117 0.(Comments:)ashow
-334 162 gm
-0.06652 0. 32 0.00665 0.(MFOLD passes it's output to a program Zuk_to_gen that translates the secondary)awidthshow
-345 162 gm
--0.01971 0.(structure prediction to a nested bracket \([]\) notation.  This notation can then be used)ashow
-356 162 gm
--0.00996 0.(in the Highlight Helix, and Draw Secondary structure \(LoopTool\) functions.)ashow
-378 162 gm
--0.01683 0.(MFOLD currently does not support much in the way of additional parameters.)ashow
-389 162 gm
--0.04089 0.(We hope to have all additional parameters available soon.)ashow
-F T cp
-%%Page: ? 21
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(21)show
-92 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.01799 0.(Blast - Basic Local Alignment Search Tool)ashow
-114 90 gm
--0.25508 0.(Reference:)ashow
-125 162 gm
-0.16143 0. 32 0.01614 0.(Karlin, Samuel and Stephen F. Altschul \(1990\).  Methods  for)awidthshow
-136 162 gm
--0.04147 0.(assessing the statistical significance of molecular sequence)ashow
-147 162 gm
--0.01135 0.(features by using general scoring schemes, Proc. Natl. Acad.)ashow
-158 162 gm
-0.51742 0. 32 0.05174 0.(Sci. USA 87:2264-2268.)awidthshow
-180 90 gm
-0.46295 0. 32 0.04629 0.(     )awidthshow
-180 162 gm
-0.27801 0. 32 0.02780 0.(Altschul, Stephen F., Warren Gish, Webb  Miller,  Eugene  W.)awidthshow
-191 90 gm
-0.46295 0. 32 0.04629 0.(     )awidthshow
-191 162 gm
-0.10040 0. 32 0.01004 0.(Myers,  and  David  J. Lipman \(1990\).  Basic local alignment)awidthshow
-202 90 gm
-0.46295 0. 32 0.04629 0.(     )awidthshow
-202 162 gm
-0.45684 0. 32 0.04568 0.(search tool, J. Mol. Biol.  215:403-410.)awidthshow
-224 90 gm
-0.46875 0. 32 0.04687 0.(   )awidthshow
-224 162 gm
-0.40649 0. 32 0.04064 0.(Altschul,  Stephen  F.  \(1991\).   Amino  acid   substitution)awidthshow
-235 90 gm
-0.46875 0. 32 0.04687 0.(   )awidthshow
-235 162 gm
-0.10742 0. 32 0.01074 0.(matrices  from an information theoretic perspective. J. Mol.)awidthshow
-246 90 gm
-0.46295 0. 32 0.04629 0.(     )awidthshow
-246 162 gm
-0.43884 0. 32 0.04388 0.(Biol.  219:555-565.)awidthshow
-290 90 gm
--0.11924 0.(Parameters:)ashow
-301 162 gm
--0.13816 0.(Which Database)ashow
-301 270 gm
--0.09788 0.(Which nucleic or amino acid database)ashow
-312 270 gm
--0.03448 0.(to search.)ashow
-334 162 gm
--0.18505 0.(Word Size)ashow
-334 270 gm
-0.17608 0. 32 0.01760 0.(Length of initial hit. after locating a match of)awidthshow
-345 270 gm
-0.27908 0. 32 0.02790 0.(this length, alignment extension is attempted.)awidthshow
-356 126 gm
--0.11082 0.(Blastn)ashow
-367 162 gm
--0.11381 0.(Match score)ashow
-367 270 gm
--0.03680 0.(Score for matches in secondary alignment extension)ashow
-378 162 gm
--0.04492 0.(Mismatch score)ashow
-378 270 gm
--0.02404 0.(Score for mismatches in secondary alignment extension)ashow
-400 126 gm
-0.49514 0. 32 0.04951 0.(Blastx, tblastn, blastp,  blast3)awidthshow
-411 162 gm
-0.69580 0. 32 0.06958 0.(Substitution Matrix)awidthshow
-411 270 gm
-0.38192 0. 32 0.03819 0.(PAM120 or PAM250)awidthshow
-444 126 gm
-0.11117 0.(Comments:)ashow
-444 198 gm
--0.01263 0.(The report is loaded into a text editor.  This should be saved as a new file)ashow
-455 198 gm
--0.01432 0.(as the default file is removed after execution.  The latest version of blast can)ashow
-466 198 gm
-0.30914 0. 32 0.03091 0.(be obtained via anonymous ftp to ncbi.nlm.nih.gov.)awidthshow
-F T cp
-%%Page: ? 22
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(22)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.14083 0. 32 0.01408 0.(FastA - Similarity search)awidthshow
-103 126 gm
--0.25508 0.(Reference:)ashow
-114 162 gm
-0.31677 0. 32 0.03167 0.(W.  R.  Pearson  and D. J. Lipman \(1988\),)awidthshow
-125 162 gm
--0.00869 0.("Improved Tools for Biological Sequence Analysis", PNAS  85:2444-2448)ashow
-147 162 gm
-0.01358 0. 32 0.00135 0.(W.  R.   Pearson \(1990\) "Rapid and Sensitive Sequence)awidthshow
-158 162 gm
-0.26550 0. 32 0.02655 0.(Comparison with FASTP and FASTA" Methods  in  Enzymology  183:63-98)awidthshow
-180 126 gm
--0.11924 0.(Parameters:)ashow
-191 162 gm
--0.23434 0.(Database)ashow
-191 306 gm
--0.12551 0.(Which database to search)ashow
-202 162 gm
-0.05493 0. 32 0.00549 0.(Number of alignments to report)awidthshow
-213 162 gm
-(SMATRIX)show
-213 306 gm
-0.26260 0. 32 0.02626 0.(Which similarity matrix to use)awidthshow
-246 126 gm
-0.11117 0.(Comments:)ashow
-257 90 gm
-0.47622 0. 32 0.04762 0.(  )awidthshow
-257 162 gm
--0.05303 0.(The FastA package includes several additional programs for pairwise alignment.)ashow
-268 162 gm
--0.00224 0.(We have only included a bare bones link to FastA.  We hope to include a more)ashow
-279 162 gm
--0.00607 0.(complete setup for the actual 2.0 release.)ashow
-F T cp
-%%Page: ? 23
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(23)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.38360 0. 32 0.03836 0.(Assemble Contigs - CAP Contig Assembly Program)awidthshow
-103 126 gm
--0.04878 0.(Author - Xiaoqiu Huang)ashow
-114 162 gm
--0.03823 0.(Department of Computer Science)ashow
-125 162 gm
--0.02279 0.(Michigan Technological University)ashow
-136 162 gm
-0.34759 0. 32 0.03475 0.(Houghton, MI 49931)awidthshow
-147 162 gm
--0.01989 0.(E-mail: huang@cs.mtu.edu)ashow
-169 162 gm
-0.31494 0. 32 0.03149 0.(Minor modifications for I/O by S. Smith)awidthshow
-191 126 gm
--0.23449 0.(Reference -)ashow
-202 162 gm
-0.05538 0. 32 0.00553 0.("A Contig Assembly Program Based on Sensitive Detection of)awidthshow
-213 90 gm
-( )show
-213 162 gm
-0.00946 0. 32 0.00094 0.(Fragment Overlaps" \(submitted to Genomics, 1991\))awidthshow
-235 126 gm
--0.11924 0.(Parameters:)ashow
-246 162 gm
-0.21423 0. 32 0.02142 0.(Minimum overlap)awidthshow
-246 306 gm
--0.11988 0.(Number of bases required for overlap)ashow
-257 162 gm
--0.01672 0.(Percent match within overlap)ashow
-257 306 gm
--0.10456 0.(Percentage match required in the overlap)ashow
-268 306 gm
--0.07734 0.(region before merge is alowwed.)ashow
-290 126 gm
-0.11117 0.(Comments:)ashow
-312 162 gm
--0.06814 0.(CAP returns the aligned sequences to the current editor window.  The sequences are)ashow
-323 162 gm
-0.00427 0. 32 0.00042 0.(placed into contigs by setting the groupid.  Cap does not change the order of the)awidthshow
-334 162 gm
--0.05079 0.(sequences, and so the results should be sorted by group and offset \(see sort under the)ashow
-345 162 gm
--0.02096 0.(Edit menu\).)ashow
-F T cp
-%%Page: ? 24
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(24)show
-92 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.10661 0.(Lsadt - Least squares additive tree analysis)ashow
-114 90 gm
-0.18157 0. 32 0.01815 0.(Author: Geert De Soete, 'C' implementation by Mike Maciukenas University of Illinois)awidthshow
-136 90 gm
--0.00590 0.(Reference:LSADT, 1983 Psychometrika, 1984 Quality and Quantity)ashow
-158 90 gm
--0.11924 0.(Parameters:)ashow
-169 162 gm
--0.02085 0.(Distance correction to use in distance matrix calculations \(see count below\).)ashow
-180 162 gm
--0.03211 0.(What should be used for initial parameters estimates)ashow
-191 162 gm
--0.12921 0.(Random number seed)ashow
-202 162 gm
--0.05371 0.(Display method \(See TreeTool below\))ashow
-224 90 gm
-0.11117 0.(Comments:)ashow
-235 162 gm
--0.02113 0.(The program has been rewritten in 'C' and will be included with the rRNA Database)ashow
-246 162 gm
-0.03906 0. 32 0.00390 0.(phylogenetic package being written at the University of Illinois Department  of)awidthshow
-257 162 gm
-0.04248 0.(Microbiology.)ashow
-279 162 gm
--0.01466 0.(Count is a  short program to calculate a distance matrix from a sequence)ashow
-290 162 gm
--0.01652 0.(alignment \(see below\).)ashow
-334 90 gm
--0.00831 0.(Count - Distance matrix calculator)ashow
-356 90 gm
-0.45852 0. 32 0.04585 0.(Author: Steven Smith)awidthshow
-378 90 gm
--0.11924 0.(Parameters:)ashow
-389 162 gm
--0.07836 0.(Correction method)ashow
-389 306 gm
--0.01190 0.(Currently Jukes-Cantor or none)ashow
-400 162 gm
--0.17300 0.(Include dashed columns)ashow
-411 162 gm
--0.04403 0.(Match upper case to lower)ashow
-444 90 gm
-0.11117 0.(Comments:)ashow
-455 162 gm
--0.02917 0.(Passes back a distance matrix in a format readable by LSADT.)ashow
-510 90 gm
--0.06629 0.(Treetool - Tree drawing/manipulation)ashow
-532 90 gm
--0.01724 0.(Author:)ashow
-532 126 gm
-0.06912 0. 32 0.00691 0.(Michael Maciukenas, University of Illinois)awidthshow
-554 90 gm
-0.11117 0.(Comments:)ashow
-565 162 gm
--0.08711 0.(See included documentation for TreeTool usage.)ashow
-F T cp
-%%Page: ? 25
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(25)show
-81 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-0.08056 0. 32 0.00805 0.(Phylip - Complete phylogenetic analysis package \(3.4\))awidthshow
-103 90 gm
-0.13824 0. 32 0.01382 0.(Author: Joe Felsenstein)awidthshow
-125 90 gm
--0.25508 0.(Reference:)ashow
-125 162 gm
-0.12664 0. 32 0.01266 0.(Felsenstein, J.  1989.  PHYLIP -- Phylogeny Inference Package \(Version 3.2\).)awidthshow
-136 162 gm
-0.18722 0. 32 0.01872 0.(Cladistics  5: 164-166)awidthshow
-169 90 gm
-0.11117 0.(Comments:)ashow
-180 162 gm
-0.13565 0. 32 0.01356 0.(Phylip is a very complete set of programs for phylogenetic analysis.  GDE)awidthshow
-191 162 gm
--0.00163 0.(simply formats selected data \(obeying any selection mask\) to Phylip, and runs)ashow
-202 162 gm
-0.06301 0. 32 0.00630 0.(the chosen program.  Although all programs from Phylip are included, only)awidthshow
-213 162 gm
-0.11154 0. 32 0.01115 0.(the programs pertaining to DNA/AA analysis are tied in to the menu system.)awidthshow
-224 162 gm
--0.06831 0.(The complete set of documentation is included, and can be viewed directly from)ashow
-235 162 gm
--0.00129 0.(GDE.  It is strongly suggested that user read the documentation before attempting to)ashow
-246 162 gm
-(interpret results.)show
-268 162 gm
--0.02252 0.(The full source code for Phylip can be obtained from genetics.washington.edu using)ashow
-279 162 gm
-0.34255 0. 32 0.03425 0.(anonymous ftp.)awidthshow
-F T cp
-%%Page: ? 26
-op
-31 30 xl
-1 1 pen
-753 90 gm
-(nc 31 30 761 582 6 rc)kp
-0 gr
-T 1 setTxMode
-0 fs
-{}mark T /Times-Roman /|______Times-Roman 0 rf
-7 fz
-2 F /|______Times-Roman fnt
-0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
-753 300 gm
-12 fz
-2 F /|______Times-Roman fnt
-(26)show
-92 90 gm
--0.10993 0.(Copyright Notice)ashow
-115 90 gm
-10 fz
-2 F /|______Times-Roman fnt
--0.01510 0.(The Genetic Data Environment \(GDE\) software and documentation are not in the public domain.  Portions)ashow
-126 90 gm
--0.04327 0.(of this code are owned and copyrighted by the The Board of Trustees of the University of Illinois and by)ashow
-137 90 gm
--0.03067 0.(Steven Smith at the Harvard Genome Laboratory.  This release of the GDE program and documentation)ashow
-148 90 gm
--0.00248 0.(may not be sold, or incorporated into a commercial product, in whole or in part without the expressed)ashow
-159 90 gm
-0.24673 0. 32 0.02467 0.(written consent of the University of Illinois and of its author, Steven Smith.)awidthshow
-181 90 gm
--0.01826 0.(All interested parties may redistribute the GDE as long as all copies are accompanied by this)ashow
-192 90 gm
-0.05432 0. 32 0.00543 0.(documentation,  and all copyright notices remain intact.  Parties interested in redistribution must do so on a)awidthshow
-203 90 gm
--0.03430 0.(non-profit basis, charging only for cost of media.  Modifications to the GDE core editor should be forwarded)ashow
-214 90 gm
-0.04577 0. 32 0.00457 0.(to the author Steven Smith at the address given below for inclusion into future releases.  External programs)awidthshow
-225 90 gm
--0.02499 0.(used by the GDE are copyright by, and are the property of their respective authors unless otherwise stated.)ashow
-258 90 gm
-0.02899 0. 32 0.00289 0.(While all attempts have been made to insure the integrity of these programs:)awidthshow
-280 90 gm
-12 fz
-2 F /|______Times-Roman fnt
--0.29307 0.(Disclaimer)ashow
-303 90 gm
-10 fz
-2 F /|______Times-Roman fnt
-(THE UNIVERSITY OF ILLINOIS, HARVARD UNIVERSITY AND THE AUTHOR, STEVEN SMITH)show
-314 90 gm
-0.21240 0. 32 0.02124 0.(GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND)awidthshow
-325 90 gm
--0.03628 0.(DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF)ashow
-336 90 gm
-0.20996 0. 32 0.02099 0.(MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE.  User)awidthshow
-347 90 gm
--0.06015 0.(understands the software is a research tool for which no warranties as to capabilities or accuracy are made,)ashow
-358 90 gm
--0.01759 0.(and user accepts the software "as is."  User assumes the entire risk as to the results and performance of the)ashow
-369 90 gm
--0.05845 0.(software and documentation.  The above parties cannot be held liable for any direct, indirect, consequential)ashow
-380 90 gm
--0.00201 0.(or incidental damages with respect to any claim by user or any third party on account of, or arising from the)ashow
-391 90 gm
--0.05157 0.(use of software and associated materials.  This disclaimer covers both the GDE core editor and all external)ashow
-402 90 gm
--0.01464 0.(programs used by the GDE.)ashow
-F T cp
-%%Trailer
-cd
-end
-%%Pages: 26 0
-%%EOF
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..644daa6
--- /dev/null
+++ b/README.md
@@ -0,0 +1,11 @@
+# Genetic Data Environment
+
+GDE is originally distributed under SunOS in the 1990s by [Eisen](https://doi.org/10.1385/0-89603-358-9:13).
+
+This software is fixed from [Oliveira et al. (2003)](http://dx.doi.org/10.1093/bioinformatics/19.1.153) and re-distributed here.
+
+# Usage
+
+Though the dependency of GDE, xview, is orphaned by quite a lot of distributions, I still fix the software to give an outlook of how biologists worked during the last centenary.
+
+To use it, you must install xview lib and include. xview hardly work well on x86_64 architecture.
diff --git a/bin/CAP2 b/bin/CAP2
deleted file mode 100755
index e239ab7..0000000
Binary files a/bin/CAP2 and /dev/null differ
diff --git a/bin/Install.csh b/bin/Install.csh
deleted file mode 100755
index 9845227..0000000
--- a/bin/Install.csh
+++ /dev/null
@@ -1,53 +0,0 @@
-#/bin/csh
-
-mkdir bin
-
-#echo "Making blast..."
-#cd BLAST
-#Install.sh
-#cd ..
-
-echo "Making clustal..."
-cd CLUSTAL
-make
-cd ..
-
-echo "Making core GDE editor"
-cd CORE
-install.csh
-cd ..
-
-echo "Making FASTA"
-cd FASTA
-install.csh
-cd ..
-
-echo "Making Harvard Genome Lab functions"
-cd HGL_SRC
-install.csh
-cd ..
-
-echo "Making looptool"
-cd LOOPTOOL
-make
-cd ..
-
-echo "Making PHYLIP"
-cd PHYLIP
-install.csh
-cd ..
-
-echo "Making ReadSeq"
-cd READSEQ
-install.csh
-cd ..
-
-echo "Making other support programs"
-cd SUPPORT
-make
-cd ..
-
-echo "Making Zuker MFOLD"
-cd ZUKER
-install.csh
-cd ..
diff --git a/bin/LoopTool b/bin/LoopTool
deleted file mode 100755
index 3b32028..0000000
Binary files a/bin/LoopTool and /dev/null differ
diff --git a/bin/Restriction b/bin/Restriction
deleted file mode 100755
index adcceec..0000000
Binary files a/bin/Restriction and /dev/null differ
diff --git a/bin/Zuk_to_gen b/bin/Zuk_to_gen
deleted file mode 100755
index 4916b60..0000000
Binary files a/bin/Zuk_to_gen and /dev/null differ
diff --git a/bin/count b/bin/count
deleted file mode 100755
index a9eeec2..0000000
Binary files a/bin/count and /dev/null differ
diff --git a/bin/fasta2VESPA.pl b/bin/fasta2VESPA.pl
deleted file mode 100755
index 38c836e..0000000
--- a/bin/fasta2VESPA.pl
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/perl
-
-
-##############################################################
-# @author    : Wagied Davids
-# @progname  : fasta2snap.pl
-# @proglang  : Perl script
-# @purpose   : Fasta to SNAP format converter
-# @input     : Fasta format files
-# @output    : SNAP format files
-# @date      : 05.08.2001
-# @version   : 0.001
-##############################################################
-
-
-
-use strict;
-
-my ($fileIN,$fileOUT);
-my ($de,@seq);
-my $seq;
-
-$fileIN= "infile";
-#$fileOUT=" ";
-
-open( FHIN, "$fileIN") || die "Error:$!";
-#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
-
-$/="%"; #input record seperator
-
-while(<FHIN>){
-  
-  ($de,@seq)=split;
-  $seq=join("",@seq);
-  $seq= uc($seq);
-
-  
-    $seq= substr($seq,0,-1); #> remaining at the end
-    print "$de\t\t$seq\n"; 
-   #print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-    #print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-
-
-}
-close(FHIN);
-#close(FHOUT);
-
diff --git a/bin/fasta2VESPA.pl~ b/bin/fasta2VESPA.pl~
deleted file mode 100755
index f384694..0000000
--- a/bin/fasta2VESPA.pl~
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/perl
-
-
-##############################################################
-# @author    : Wagied Davids
-# @progname  : fasta2snap.pl
-# @proglang  : Perl script
-# @purpose   : Fasta to SNAP format converter
-# @input     : Fasta format files
-# @output    : SNAP format files
-# @date      : 05.08.2001
-# @version   : 0.001
-##############################################################
-
-
-
-use strict;
-
-my ($fileIN,$fileOUT);
-my ($de,@seq);
-my $seq;
-
-$fileIN= "infile";
-#$fileOUT=" ";
-
-open( FHIN, "$fileIN") || die "Error:$!";
-#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
-
-$/="%"; #input record seperator
-
-while(<FHIN>){
-  
-  ($de,@seq)=split;
-  $seq=join("",@seq);
-  $seq= uc($seq);
-
-  
-    $seq= substr($seq,0,-1); #> remaining at the end
-    print "$de\t$seq\n"; 
-   #print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-    #print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-
-
-}
-close(FHIN);
-#close(FHOUT);
-
diff --git a/bin/fasta2snap.pl b/bin/fasta2snap.pl
deleted file mode 100755
index 76b358d..0000000
--- a/bin/fasta2snap.pl
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/perl
-
-
-##############################################################
-# @author    : Wagied Davids
-# @progname  : fasta2snap.pl
-# @proglang  : Perl script
-# @purpose   : Fasta to SNAP format converter
-# @input     : Fasta format files
-# @output    : SNAP format files
-# @date      : 05.08.2001
-# @version   : 0.001
-##############################################################
-
-
-
-use strict;
-
-my ($fileIN,$fileOUT);
-my ($de,@seq);
-my $seq;
-
-$fileIN= "infile";
-#$fileOUT=" ";
-
-open( FHIN, "$fileIN") || die "Error:$!";
-#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
-
-$/="#"; #input record seperator
-
-while(<FHIN>){
-  
-  ($de,@seq)=split;
-  $seq=join("",@seq);
-  $seq= uc($seq);
-
-  
-    $seq= substr($seq,0,-1); #> remaining at the end
-    print "$de\t$seq\n"; 
-   #print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-    #print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-
-
-}
-close(FHIN);
-#close(FHOUT);
-
diff --git a/bin/fasta2snap.pl~ b/bin/fasta2snap.pl~
deleted file mode 100755
index 38f5ca0..0000000
--- a/bin/fasta2snap.pl~
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/perl
-
-
-##############################################################
-# @author    : Wagied Davids
-# @progname  : fasta2snap.pl
-# @proglang  : Perl script
-# @purpose   : Fasta to SNAP format converter
-# @input     : Fasta format files
-# @output    : SNAP format files
-# @date      : 05.08.2001
-# @version   : 0.001
-##############################################################
-
-
-
-use strict;
-
-my ($fileIN,$fileOUT);
-my ($de,@seq);
-my $seq;
-
-$fileIN= "infile";
-#$fileOUT=" ";
-
-open( FHIN, "$fileIN") || die "Error:$!";
-#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
-
-$/=">"; #input record seperator
-
-while(<FHIN>){
-  
-  ($de,@seq)=split;
-  $seq=join("",@seq);
-  $seq= uc($seq);
-
-  
-    $seq= substr($seq,0,-1); #> remaining at the end
-    print "$de\t$seq\n"; 
-   #print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-    #print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
-
-
-}
-close(FHIN);
-#close(FHOUT);
-
diff --git a/bin/findall b/bin/findall
deleted file mode 100755
index 7f200bc..0000000
Binary files a/bin/findall and /dev/null differ
diff --git a/bin/gde b/bin/gde
deleted file mode 100755
index 3d64405..0000000
Binary files a/bin/gde and /dev/null differ
diff --git a/bin/installBLASTDB.pl b/bin/installBLASTDB.pl
deleted file mode 100755
index 7deadc0..0000000
--- a/bin/installBLASTDB.pl
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $newFileName;
-my $line;
-
-my $sourceFile = shift;
-my $menuName = shift;
-
-print("mv -f ./$sourceFile.* /usr/local/bio/db/\n");
-print("cp -f ./$sourceFile /usr/local/bio/db/\n");
-
-
-
-print system("mv -f ./$sourceFile.* /usr/local/bio/db/");
-# or die ("cannot copy files\n");
-print system("cp -f ./$sourceFile /usr/local/bio/db/") ;
-#or die ("cannot copy file\n");
-
-
-open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^arg:BLASTDBDNA/){
-	    print "FOUND\n";
-	    while (<MENUFILE>){
-		print NEWFILE;
-		if (/^argchoice:/){
-		    print NEWFILE "argchoice:$menuName:/usr/local/bio/db/$sourceFile\n";
-		    last READLOOP;
-		}
-	    }
-	}
-    }
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-print "new file: $newFileName\n";
-system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/installBLASTDB.pl~ b/bin/installBLASTDB.pl~
deleted file mode 100755
index 977e53b..0000000
--- a/bin/installBLASTDB.pl~
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $newFileName;
-my $line;
-
-my $sourceFile = shift;
-my $menuName = shift;
-
-print("mv -f ./$sourceFile.* /usr/local/biotools/db/\n");
-print("cp -f ./$sourceFile /usr/local/biotools/db/\n");
-
-
-
-print system("mv -f ./$sourceFile.* /usr/local/biotools/db/");
-# or die ("cannot copy files\n");
-print system("cp -f ./$sourceFile /usr/local/biotools/db/") ;
-#or die ("cannot copy file\n");
-
-
-open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^arg:BLASTDBDNA/){
-	    print "FOUND\n";
-	    while (<MENUFILE>){
-		print NEWFILE;
-		if (/^argchoice:/){
-		    print NEWFILE "argchoice:$menuName:/usr/local/biotools/db/$sourceFile\n";
-		    last READLOOP;
-		}
-	    }
-	}
-    }
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-print "new file: $newFileName\n";
-system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/installBLASTDBPROT.pl b/bin/installBLASTDBPROT.pl
deleted file mode 100755
index f1cd486..0000000
--- a/bin/installBLASTDBPROT.pl
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $newFileName;
-my $line;
-
-my $sourceFile = shift;
-my $menuName = shift;
-
-print("mv -f ./$sourceFile.* /usr/local/bio/db/\n");
-print("cp -f ./$sourceFile /usr/local/bio/db/\n");
-
-
-
-print system("mv -f ./$sourceFile.* /usr/local/bio/db/");
-# or die ("cannot copy files\n");
-print system("cp -f ./$sourceFile /usr/local/bio/db/") ;
-#or die ("cannot copy file\n");
-
-
-open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^arg:BLASTDBPROT/){
-	    print "FOUND\n";
-	    while (<MENUFILE>){
-		print NEWFILE;
-		if (/^argchoice:/){
-		    print NEWFILE "argchoice:$menuName:/usr/local/bio/db/$sourceFile\n";
-		    last READLOOP;
-		}
-	    }
-	}
-    }
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-print "new file: $newFileName\n";
-system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/installBLASTDBPROT.pl~ b/bin/installBLASTDBPROT.pl~
deleted file mode 100755
index fcb8c41..0000000
--- a/bin/installBLASTDBPROT.pl~
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $newFileName;
-my $line;
-
-my $sourceFile = shift;
-my $menuName = shift;
-
-print("mv -f ./$sourceFile.* /usr/local/biotools/db/\n");
-print("cp -f ./$sourceFile /usr/local/biotools/db/\n");
-
-
-
-print system("mv -f ./$sourceFile.* /usr/local/biotools/db/");
-# or die ("cannot copy files\n");
-print system("cp -f ./$sourceFile /usr/local/biotools/db/") ;
-#or die ("cannot copy file\n");
-
-
-open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^arg:BLASTDBPROT/){
-	    print "FOUND\n";
-	    while (<MENUFILE>){
-		print NEWFILE;
-		if (/^argchoice:/){
-		    print NEWFILE "argchoice:$menuName:/usr/local/biotools/db/$sourceFile\n";
-		    last READLOOP;
-		}
-	    }
-	}
-    }
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-print "new file: $newFileName\n";
-system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/lsadt b/bin/lsadt
deleted file mode 100755
index 1b4d297..0000000
Binary files a/bin/lsadt and /dev/null differ
diff --git a/bin/newDATASET.pl b/bin/newDATASET.pl
deleted file mode 100755
index d936ace..0000000
--- a/bin/newDATASET.pl
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/perl 
-
-
-my $name = shift;
-my $file = shift;
-
-open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^menu:seq. datasets/){
-	    print "FOUND\n";
-	    print NEWFILE "item:$name\n";
-	    print NEWFILE "itemmethod:readseq /usr/local/bio/GDE/db/$file -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp\n";
-	    print NEWFILE "out:OUTPUTFILE\n";
-	    print NEWFILE "outformat:genbank\n\n";\
-		    last READLOOP;
-		
-	    }
-	}
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-
-system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/newDATASET.pl~ b/bin/newDATASET.pl~
deleted file mode 100755
index e014012..0000000
--- a/bin/newDATASET.pl~
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/perl 
-
-
-my $name = shift;
-my $file = shift;
-
-open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^menu:seq. datasets/){
-	    print "FOUND\n";
-	    print NEWFILE "item:$name\n";
-	    print NEWFILE "itemmethod:readseq /usr/local/biotools/GDE/db/$file -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp\n";
-	    print NEWFILE "out:OUTPUTFILE\n";
-	    print NEWFILE "outformat:genbank\n\n";\
-		    last READLOOP;
-		
-	    }
-	}
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-
-system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/newURL.pl b/bin/newURL.pl
deleted file mode 100755
index 468f112..0000000
--- a/bin/newURL.pl
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/perl 
-
-
-my $urlname = shift;
-my $url = shift;
-
-open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^menu:On-Line/){
-	    print "FOUND\n";
-	    print NEWFILE "item:$urlname\n";
-	    print NEWFILE "itemmethod:netscape $url &\n";
-		    last READLOOP;
-		
-	    }
-	}
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-
-system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/newURL.pl~ b/bin/newURL.pl~
deleted file mode 100755
index ccfb52b..0000000
--- a/bin/newURL.pl~
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/perl 
-
-
-my $urlname = shift;
-my $url = shift;
-
-open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot open menu file, sorry\n";
-$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
-open(NEWFILE, ">$newFileName");
- READLOOP:
-    while (<MENUFILE>){
-	print NEWFILE;
-	if (/^menu:On-Line/){
-	    print "FOUND\n";
-	    print NEWFILE "item:$urlname\n";
-	    print NEWFILE "itemmethod:netscape $url &\n";
-		    last READLOOP;
-		
-	    }
-	}
-while (<MENUFILE>){
-    print NEWFILE;
-}
-close(NEWFILE);
-close(MENUFILE);
-
-system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
-    or die "cannot replace old menu file\n";
-
-
-
-
-
-
diff --git a/bin/readseq b/bin/readseq
deleted file mode 100755
index ba1b981..0000000
Binary files a/bin/readseq and /dev/null differ
diff --git a/bin/sho_helix b/bin/sho_helix
deleted file mode 100755
index 0c953a3..0000000
Binary files a/bin/sho_helix and /dev/null differ
diff --git a/bin/varpos b/bin/varpos
deleted file mode 100755
index 801dbf0..0000000
Binary files a/bin/varpos and /dev/null differ