190 lines
6.7 KiB
Text
190 lines
6.7 KiB
Text
Release Notes for Staden Package 1992.3
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---------------------------------------
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Installation guide
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------------------
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The file doc/install.PS contain installation instructions.
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Manual for the Staden Package
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-----------------------------
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There is now a 135 page manual on the Staden Package. It is currently
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being distributed on a Word4 document on a Macintosh floppy disk.
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Feedback and bug reports
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------------------------
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We welcome comments and suggestions on all aspects of the package and are
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best contacted by email: rs@uk.ac.cam.mrc-lmb and sd@uk.ac.cam.mrc-lmb.
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All abnormal terminations are bugs and we would like to be told of them
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so they can be fixed. We recommend that you request an update at least once
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a year as the package is evolving very rapidly.
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Note due to popular demand we have decided to release new routines earlier
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than in the past so please report bugs. The documentation for additions may
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be sparser than before, or non-existent, but if there is something with which
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you need help, email us.
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Changes this release
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--------------------
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The assembly programs bap and xbap heve several new functions:
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1. Find single stranded regions and try to fill them with "hidden"
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data from the adjacent readings.
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2. Find single stranded regions (includes ends of contigs) and
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select primers and templates for double stranding them (joining
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them).
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3. Pre assembly screening for readings to find those that align
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best. Optionally the hidden data can also be included in the
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comparison (part of assembly function).
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4. Find pairs of readings taken from opposite ends of the same
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template (ie forward and reverse read pairs). List or plot their
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positions.
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5. A new function to check that readings have been assembled into
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the correct positions. It aligns the hidden (previously termed "unused")
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parts of readings with the consensus they overlap to see how well
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they align. Poor alignments are reported.
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6. During assembly each reading is now allowed to match up to 100
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different places.
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It might be guessed from the above that we are trying to improve our
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ability to deal with the assembly of human data. Hence, also the next
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addition.
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A new experimental program (rep) for screening readings for Alu
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sequences prior to assembly. The Alu containing segments are tagged
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so they can be seen in the contig editor. A library of Alu sequences
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is included in /tables/alus. The program is quite slow as it compares
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each reading in both orientations with all of the Alu sequences (126
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of them) in order to find the best match. Only time and more data will
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tell how sensitive it is, and whether the current default score 0f 0.6
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is "correct". BEWARE rep modifies the original reading files to include
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the tag information. The only information is in /help/alu.help
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A new program for extracting sets of sequences and their annotations
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from the sequence libraries (lip). The only information is in
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/help/lip.help
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Changes to the xterm userinterface. These routines have been completely
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rewritten. One addition is that now ?? in response to a question will
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allow the user to get help on any function in a program. help is also
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improved in the x version.
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Changes last release
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--------------------
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DAP, XDAP have been replaced by BAP and XBAP (see below)
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A new function for examining repeats has been added to NIP
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A new repeat search has been added to SIP
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Some outputs have been changed to produce FASTA format files
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instead of PIR.
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MEP now allows searches for motifs in which any 8 out of a string
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of 20 can be switched on.
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The manual has been updated.
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Keyword and author searches on sequence libraries
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All programs that use the libraries can now perform author
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and keyword searches on all libraries (only nip did so before).
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Postscript output
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All graphics can now be saved to disk in postscript form by
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use of a sub-option in "Redirect output".
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Sequence assembly
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BAP, XBAP replace DAP and XDAP. A program to convert DAP databases to BAP
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databases (convert) is included. BAP databases can contain up to 8000 readings
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and a consensus of 500,000 bases. A minor edit and recompilation will allow
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up to 99,999 readings. The space is used more efficiently now as the databases
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grow as the number of readings increases. Reading names can be 16 characters
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in length. In addition:
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1) Assembly is 4 times as fast as in the DAP.
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2) Find internal joins is 5 times as fast and now brings up the join editor
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with the two contigs in the correct orientation and aligned.
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3) The assembly routines align pads better, plus a new automatic function can
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also be used to align them prior to editing.
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4) The contig editor has been greatly speeded up and its functionality
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has been enhanced.
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5) A routine for selecting oligos for primer walking is included.
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6) A new routine allows batches of readings to be removed from a database.
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7) We have also included routines for making SCF files, for getting the
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sequence from SCF files, and one for marking the poor quality data in
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readings. See the manual.
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Sequence library formats
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The standard sequence library indexing method is now that used on the
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EMBL CD-ROM. The libraries (EMBL nucleotide and SWISSPROT protein) can be
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left on the CD-ROM or copied to disk. We include in the package programs
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for creating this type of index for EMBL updates, PIR in codata format,
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NRL3D and GenBank. If the indexes are created all programs can read all
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these libraries. Programs and scripts for this task are contained in the
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directory indexseqlibs.
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The keyword and author searches are particularly fast and the
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keyword index is based on ALL text in the files - not just the keywords.
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Feature table formats
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The programs now use the new feature table format common to EMBL
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and GenBank, but retain the old format for SWISSPROT which has not yet
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changed.
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For details of the above see file SequenceLibraries.
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Pattern searches
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Pipl and Nipl now have the facility to find only the best scoring
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match for each sequence. The prompt is "? report all matches", so typing
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only return means all matches will be shown and typing n means only the
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highest scoring will be reported. It is particularly useful when employed
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to create alignments. The corresponding help file has not been updated.
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Also to incorporate long unix file names the pattern files no longer include
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the annotation "filename".
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Nip
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Option 38 in nip "translate and list" has been removed as the the
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more flexible routines of option 39 incorporate all its functionality. Many
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options that relate to feature tables have been modified but their help files
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are not yet up to date.
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Vep
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A program (vep) for automatic excising of vector (either
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sequencing vector or cosmid vector) sequences from readings is now
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included in the package.
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Rodger Staden, Simon Dear, James Bonfield
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