%!
%%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
%%BeginProcSet: "(AppleDict md)" 70 0
statusdict begin product(LaserWriter II NT)eq revision 1 eq and
{userdict begin/oldcds/cleardictstack load def/cleardictstack{31 sendpcmd 4 eq tonerlight/oldcds load  exec}bind def
end
currentfile eexec
}{save currentfile 359 string readhexstring pop pop restore}ifelse
35de8eabfc7fa5eac0431edc501ad43f5fcbdf9fdd321cce93b525f4439dd94696bf56ac13a0a2aad1e6bcf444711e941d7217138d20ae0500145f815439cc14e697ad201df728ea4ccad4ac
331aa03a7aacde10760bf4ee12bbf73c77cdcbf1796f26f0dd255d2407e1ac41
d27489a69d6b69c6a841468b46720b75ad65650700e0c528e7af61e7e3e821b59445c44b69831ebc9deaf0e3aecc14b7a1c2e18bc1fa42a59219f1e36f236e3d6c89114b1f231999c3dbce6b43f3e2918fcb85575941a9d1e65c86aa08e6eea86cc66ce90e5e4add57f2585e
7b1c0b5203cfc46868d6e3c0d66db79174e7091e32e307679732da062e440e41dabd36a161b611a7e4523a49694026206803dbfd5be5c5fe433f0f18a40057db6f1302848c8da4a10a7f14c6
3d512806362b1be092ad5dbd36d75fe63e4cae2ba9b72390f580cac344a08bdf6eb9e36ec45bad2a0b82829a72e0efa2d87332c482196e690361168271c55053341ab3
end
/sc {60 45 {abs exch abs 2 copy add 1 gt{1.0 sub dup mul exch 1.0 sub dup mul add 1.0 sub}{dup mul exch dup mul add 1.0 exch sub}
ifelse}setscreen} bind def statusdict begin product(LaserWriter II)anchorsearch end
{pop pop/letter [/letter load /exec load /sc load /exec load]cvx def/legal [/legal load /exec load /sc load /exec load]cvx def/a4 [/a4 load /exec load /sc load /exec load]cvx def/b5 [/b5 load /exec load /sc load /exec load]cvx def
/lettersmall [/lettersmall load /exec load /sc load /exec load]cvx def/a4small [/a4small load /exec load /sc load /exec load]cvx def/note [/note load /exec load /sc load /exec load]cvx def}{pop}ifelse
systemdict/currentpacking known{currentpacking true setpacking}if
/LW{save statusdict/product get(LaserWriter)anchorsearch
exch pop{length 0 eq{1}{2}ifelse}{0}ifelse exch restore}bind def
/LW+{LW 2 eq}bind def
/ok{systemdict/statusdict known dup{LW 0 gt and}if}bind def
ok{statusdict begin 9 sccinteractive 3 ne exch 0 ne or{9 0 3 setsccinteractive}if end}if
/md 270 dict def md begin
/av 0 def
/T true def/F false def/mtx matrix def/s75 75 string def/sa8 8 string def/sb8 8 string def
/sc8 8 string def/sd8 8 string def/s1 ( ) def/pxs 1 def/pys 1 def
/ns false def
1 0 mtx defaultmatrix dtransform exch atan/pa exch def/nlw .24 def/ppr [-32 -29.52 762 582.48] def
/pgr [0 0 0 0] def
/pgs 1 def/por true def/xb 500 array def/so true def/tso true def/fillflag false def/pnm 1 def/fmv true def
/sfl false def/ma 0 def/invertflag false def/dbinvertflag false def/xflip false def/yflip false def/noflips true def/scaleby96 false def/fNote true def/fBitStretch true def
/4colors false def/3colors false def/2colors false def
/wtkey false def
statusdict begin/waittimeout where{pop waittimeout 300 lt{md /wtkey true put}if}if end
wtkey{statusdict begin/setdefaulttimeouts where{pop 0 60 300 setdefaulttimeouts}if end}if
/fg (Rvd\001\001\000\000\177) def
/bdf{bind def}bind def
/xdf{exch def}bdf
/xl{neg exch neg translate}bdf
/fp{pnsh 0 ne pnsv 0 ne and}bdf
/nop{}bdf/lnop[/nop load]cvx bdf
/vrb[
{fp{fg 6 get 0 ne{gsave stroke grestore}{gsave 1 setlinewidth pnsh pnsv scale stroke grestore}ifelse}if newpath}bind
/eofill load
dup
/newpath load
2 index
dup
{clip newpath}bind
{}bind
dup
2 copy
]def
systemdict/currentcolorscreen known{currentcolorscreen/dkspf xdf/dkrot xdf/dkfreq xdf/dyspf xdf/dyrot xdf/dyfreq xdf/dmspf xdf/dmrot xdf/dmfreq xdf
/dcspf xdf/dcrot xdf/dcfreq xdf}{currentscreen/spf xdf/rot xdf/freq xdf}ifelse
/doop{vrb exch get exec}bdf
/psu{/udf xdf/tso xdf /fNote xdf/fBitStretch xdf/scaleby96 xdf/yflip xdf/xflip xdf
/invertflag xdf/dbinvertflag invertflag statusdict begin version cvr 47.0 ge product (LaserWriter) eq not and end invertflag and {not}if def
xflip yflip or{/noflips false def}if
/pgs xdf 2 index .72 mul exch div/pys xdf div .72 mul/pxs xdf ppr astore pop pgr astore pop/por xdf sn and/so xdf}bdf
/tab{statusdict /11x17 known{statusdict begin /11x17 load end}{statusdict /setpage known{statusdict begin 792 1224 1 setpage end}{statusdict /setpageparams known{statusdict begin 792 1224 0 1 setpageparams end}if}ifelse}ifelse}bdf
/a3Size{statusdict /a3 known{statusdict begin /a3 load end}{statusdict /setpageparams known{statusdict begin 842 1191 0 1 setpageparams end}if}ifelse}bdf
/txpose{fNote{smalls}{bigs}ifelse pgs get exec pxs pys scale ppr aload pop por{noflips{pop exch neg exch translate pop 1 -1 scale}if
xflip yflip and{pop exch neg exch translate 180 rotate 1 -1 scale ppr 3 get ppr 1 get neg sub neg ppr 2 get ppr 0 get neg sub neg translate}if 
xflip yflip not and{pop exch neg exch translate pop 180 rotate ppr 3 get ppr 1 get neg sub neg 0 translate}if yflip xflip not and{ppr 1 get neg ppr 0 get neg translate}if}
{noflips{translate pop pop 270 rotate 1 -1 scale}if xflip yflip and{translate pop pop 90 rotate 1 -1 scale ppr 3 get ppr 1 get neg sub neg ppr 2 get ppr 0 get neg sub neg translate}if
xflip yflip not and{translate pop pop 90 rotate ppr 3 get ppr 1 get neg sub neg 0 translate}if yflip xflip not and{translate pop pop 270 rotate ppr 2 get ppr 0 get neg sub neg 0 exch translate}if}ifelse
wtkey{statusdict/waittimeout 300 put}if 
scaleby96{ppr aload pop 4 -1 roll add 2 div 3 1 roll add 2 div 2 copy translate .96 dup scale neg exch neg exch translate}if}bdf
/fr{4 copy pgr aload pop 3 -1 roll add 3 1 roll exch add 6 2 roll 3 -1 roll
sub 3 1 roll exch sub 3 -1 roll exch div 3 1 roll div exch scale pop pop xl}bdf
/obl{{0.212557 mul}{pop 0}ifelse}bdf
/sfd{ps fg 5 -1 roll get mul 100 div 0 ps 5 -1 roll obl ps neg 0 0 6a astore makefont setfont}bdf
/fnt{findfont sfd}bdf
/bt{sa 3 1 roll 3 index and put}bdf
/sa(\000\000\000\000\000\000\000\000\000\000)def
/fs{0 1 bt 1 2 bt 2 4 bt 3 8 bt 4 16 bt 5 32 bt 6 64 bt 7 128 bt sa exch 8 exch put}bdf
/mx1 matrix def
/mx2 matrix def
/mx3 matrix def
/bu{currentpoint 4colors{currentcmykcolor}{currentrgbcolor}ifelse currentlinewidth currentlinecap currentlinejoin 
currentdash exch aload length fg 5 sfl{1}{0}ifelse put pnsv pnsh 
2t aload pop 3a aload pop mx2 aload pop mx1 aload pop mtx currentmatrix aload pop
mx3 aload pop ps pm restore/ps xdf mx3 astore pop}bdf
/bn{/pm save def mx3 setmatrix newpath 0 0 moveto ct dup 39 get 0 exch getinterval cvx exec mtx astore setmatrix mx1 astore pop mx2 astore pop 3a 
astore pop 2t astore pop/pnsh xdf/pnsv xdf gw
/sfl fg 5 get 0 ne def array astore exch setdash setlinejoin setlinecap 
setlinewidth 4colors{setcmykcolor}{setrgbcolor}ifelse moveto}bdf
/fc{save vmstatus exch sub 50000 lt
{(%%[|0|]%%)=print flush}if pop restore}bdf
/tc{32768 div add 3 1 roll 32768 div add 2t astore pop}bdf
/3a [0 0 0] def
/2t 2 array def
/tp{3a astore pop}bdf
/tt{mx2 currentmatrix pop currentpoint 2 copy 2t aload pop qa 2 copy translate 3a aload pop exch dup 0 eq
{pop}{1 eq{-1 1}{1 -1}ifelse scale}ifelse rotate pop neg exch neg exch translate moveto}bdf
/te{mx2 setmatrix}bdf
/th{3 -1 roll div 3 1 roll exch div 2 copy mx1 scale pop scale/sfl true def}bdf
/tu{1 1 mx1 itransform scale/sfl false def}bdf
/ts{1 1 mx1 transform scale/sfl true def}bdf
/fz{/ps xdf}bdf
/dv{dup 0 ne{div}{pop}ifelse}bdf
/pop4{pop pop pop pop}bdf
/it{sfl{mx1 itransform}if}bdf
/gm{exch it moveto}bdf/rm{it rmoveto}bdf
/lm{currentpoint sfl{mx1 transform}if exch pop sub 0 exch it rmoveto}bdf
/fm{statusdict/manualfeed known}bdf
/se{statusdict exch/manualfeed exch put}bdf
/mf{dup/ma exch def 0 gt{fm se/t1 5 st ok ma 1 gt and{/t2 0 st/t3 0 st
statusdict/manualfeedtimeout 3600 put
}if}if}bdf
/jn{/statusdict where exch pop{statusdict exch /jobname exch put}if}bdf
/pen{pnm mul/pnsh xdf pnm mul/pnsv xdf pnsh setlinewidth}bdf
/min{2 copy gt{exch}if pop}bdf
/max{2 copy lt{exch}if pop}bdf
/dh{fg 6 1 put array astore dup {1 pxs div mul exch}forall astore exch pop exch pop exch setdash}bdf
/ih[currentdash]def
/rh{fg 6 0 put ih aload pop setdash}bdf
/dl{gsave nlw pys div setlinewidth 0 setgray}bdf
/dlin{exch currentpoint currentlinewidth 2 div dup
translate newpath moveto lineto currentpoint stroke grestore moveto}bdf
/lin{fg 6 get 0 ne{exch lineto currentpoint 0 doop moveto}
{exch currentpoint/pnlv xdf/pnlh xdf gsave newpath/@1 xdf/@2 xdf fp{pnlh @2 lt{pnlv @1 ge
{pnlh pnlv moveto @2 @1 lineto pnsh 0 rlineto
0 pnsv rlineto pnlh pnsh add pnlv pnsv add lineto pnsh neg 0 rlineto}
{pnlh pnlv moveto pnsh 0 rlineto @2 pnsh add @1 lineto 0 pnsv rlineto
pnsh neg 0 rlineto pnlh pnlv pnsv add lineto}ifelse}{pnlv @1 gt
{@2 @1 moveto pnsh 0 rlineto pnlh pnsh add pnlv lineto 0 pnsv rlineto
pnsh neg 0 rlineto @2 @1 pnsv add lineto}{pnlh pnlv moveto pnsh 0 rlineto
0 pnsv rlineto @2 pnsh add @1 pnsv add lineto pnsh neg 0 rlineto
0 pnsv neg rlineto}ifelse}ifelse
closepath fill}if @2 @1 grestore moveto}ifelse}bdf
/gw{/pnm fg 3 get fg 4 get div def}bdf
/lw{fg exch 4 exch put fg exch 3 exch put gw pnsv pnsh pen}bdf
/barc{/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf
/@6 xdf/@7 xdf/@8 xdf gsave
@5 @7 add 2 div @6 @8 add 2 div translate newpath 0 0 moveto
@5 @7 sub @6 @8 sub mtx currentmatrix pop scale @1{newpath}if
0 0 0.5 @4 @3 arc @4 @3 sub abs 360 ge{closepath}if
mtx setmatrix @2 doop grestore}bdf
/ar{dup 0 eq barc}bdf
/ov{0 exch 360 exch true barc}bdf
/rc{/@t xdf currentpoint 6 2 roll newpath 4 copy 4 2 roll exch moveto
6 -1 roll lineto lineto lineto closepath @t doop moveto}bdf
/mup{dup pnsh 2 div le exch pnsv 2 div le or}bdf
/rr{/@1 xdf 2. div/@2 xdf 2. div/@3 xdf
/@4 xdf/@5 xdf/@6 xdf/@7 xdf
@7 @5 eq @6 @4 eq @2 mup or or{@7 @6 @5 @4 @1 rc}
{@4 @6 sub 2. div dup @2 lt{/@2 xdf}{pop}ifelse
@5 @7 sub 2. div dup @2 lt{/@2 xdf}{pop}ifelse
@1 0 eq{/@2 @2 pnsh 2 div 2 copy gt{sub def}{0 pop4}ifelse}if
currentpoint newpath
@4 @6 add 2. div @7 moveto
@4 @7 @4 @5 @2 arcto pop4
@4 @5 @6 @5 @2 arcto pop4
@6 @5 @6 @7 @2 arcto pop4
@6 @7 @4 @7 @2 arcto pop4
closepath @1 doop moveto}ifelse}bdf
/pr{gsave newpath/pl{exch moveto/pl{exch lineto}def}def}bdf
/pl{exch lineto}bdf
/ep{dup 0 eq{{moveto}{exch lin}{}{(%%[|1|]%%)= flush}pathforall
pop grestore}{doop grestore}ifelse currentpoint newpath moveto}bdf
/gr{64. div setgray}bdf
/savescreen{ns not{/ns true def systemdict/currentcolorscreen known{currentcolorscreen/pkspf xdf/pkrot xdf/pkfreq xdf/pyspf xdf/pyrot xdf/pyfreq xdf/pmspf xdf/pmrot xdf/pmfreq xdf
/pcspf xdf/pcrot xdf/pcfreq xdf}{currentscreen/sspf xdf/srot xdf/sfreq xdf}ifelse}if}bdf
/restorescreen{/ns false def systemdict/setcolorscreen known{pcfreq pcrot/pcspf load pmfreq pmrot/pmspf load pyfreq pyrot/pyspf load
pkfreq pkrot/pkspf load setcolorscreen}{sfreq srot/sspf load setscreen}ifelse}bdf
/pat{savescreen sa8 
copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}setscreen exch not{gr}{pop}ifelse}bdf
/sg{restorescreen gr}bdf
/cpat{savescreen 10 2 roll 7 -1 roll sa8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}8 -1 roll sb8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sb8
exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}9 -1 roll sc8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sc8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}10 -1 roll sd8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sd8
exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}psuedo1 dsc 4{4 -1 roll 1 exch 64 div sub}repeat setcmykcolor pop pop}bdf
systemdict/setcolorscreen known{/psuedo1 lnop bdf/dsc/setcolorscreen load def}{/psuedo1{16{pop}repeat sa8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}}bdf
/bwsc{setscreen dup gr 0 exch 0 exch 64 exch 64 exch 64 exch}bdf/dsc/bwsc load def
}ifelse
systemdict/setcmykcolor known not{/setcmykcolor{1 sub 4 1 roll 3{3 index add neg dup 0 lt{pop 0}if 3 1 roll}repeat setrgbcolor pop}bdf}if
/dc{transform round .5 sub exch round .5 sub exch itransform}bdf
/sn{userdict/smooth4 known}bdf
/x8{3 bitshift}bdf
/x4{2 bitshift}bdf
/d4{-2 bitshift}bdf
/d8{-3 bitshift}bdf
/rb{15 add -4 bitshift 1 bitshift}bdf
/db{/@7 save def/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf/@6 @5 @3 4 add mul def
dc translate scale/xdbit 1 1 idtransform abs/ydbit exch def abs def{0 0 1 ydbit add 1 10 rc clip}if
@1 0 eq @1 4 eq or{currentrgbcolor 1 setgray ydbit 0 1 ydbit add 1 2 rc setrgbcolor}if
@1 3 eq @1 7 eq or{1 setgray}{currentrgbcolor 2 index eq exch 2 index eq and exch pop{0 setgray}if}ifelse/@9 @1 0 eq @1 1 eq @1 3 eq or or dbinvertflag xor def/@13 @6 def
@2 fBitStretch or{/@10 @4 x4 def/@11 @3 x4 def/@12 @10 rb def/@13 @12 @11 mul def/@15 1 1 dtransform abs/calcY 1 index def round cvi/@14 exch def
abs/calcX 1 index def round cvi scaleby96 not{1 add}if def/@16 @15 rb def/@17 @16 @14 mul def}if
sn @13 60000 lt and @2 fBitStretch or and{mtx currentmatrix dup 1 get exch 2 get 0. eq exch 0. eq and @17 60000 lt and fBitStretch and{@16 3 bitshift @14 @9 [calcX 0 0 calcY 0 0]{@17 string @13 string
currentfile @6 string readhexstring pop 1 index @4 @3 @5 @12 @2 smooth4
@10 @11 @12 dup string 5 index @15 @14 @16 dup string stretch}imagemask}{@12 x8 @11 @9 [@10 0 0 @11 0 0]{@13 string
currentfile @6 string readhexstring pop 1 index @4 @3 @5 @12 @2 smooth4}imagemask}ifelse}{@5 3 bitshift @3 4 add @9 [@4 0 0 @3 0 2]{currentfile @6 string readhexstring pop}imagemask}ifelse
@7 restore}bdf
systemdict/setcmykcolor known{/psuedo lnop bdf/di/colorimage load def}{/routines[{.3 mul add 1}bind{.59 mul add 2}bind{.11 mul add round cvi str exch i exch put/i i 1 add def 0 0}bind]def
/psuedo{/i 0 def 0 exch 0 exch{exch routines exch get exec}forall pop pop str}bdf/bwi{pop pop image}bdf/di/bwi load def}ifelse
/cdb{/@7 save def/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf
systemdict/setcmykcolor known not{dc}if translate scale /@6 xdf
/@18 @5 dup 60000 ge{pop 60000}if string def @6 not{/str @18 0 @18 length 3 idiv getinterval def}if @4 @3 8 [@4 0 0 @3 0 0]@6{{currentfile @18 readhexstring pop}image}{{currentfile @18 readhexstring pop psuedo}false 3 di}ifelse @7 restore}bdf
/wd 16 dict def
/mfont 14 dict def
/mdf{mfont wcheck not{/mfont 14 dict def}if mfont begin xdf end}bdf
/cf{{1 index/FID ne{def}{pop pop}ifelse}forall}bdf/rf{/@1 exch def/@2 exch def
FontDirectory @2 known{cleartomark pop}{findfont dup begin dup length @1 add dict begin
cf{/Encoding macvec def}{Encoding dup length array copy/Encoding exch def
counttomark 2 idiv{Encoding 3 1 roll put}repeat}ifelse
pop
exec currentdict end end @2 exch definefont pop}ifelse}bdf
/bmbc{exch begin wd begin
/cr xdf
save
CharTable cr 6 mul 6 getinterval{}forall
/bitheight xdf/bitwidth xdf
.96 div/width xdf
Gkernmax add/XOffset xdf Gdescent add/YOffset xdf/rowbytes xdf
rowbytes 255 eq{0 0 0 0 0 0 setcachedevice}
{Gnormsize dup scale
width 0 XOffset YOffset bitwidth XOffset add bitheight YOffset add
setcachedevice
rowbytes 0 ne{
XOffset YOffset translate newpath 0 0 moveto
bitwidth bitheight scale
sn{
/xSmt bitwidth x4 def
/ySmt bitheight x4 def
/rSmt xSmt rb def
rSmt x8 ySmt true
[xSmt 0 0 ySmt neg 0 ySmt]
{rSmt ySmt mul string CharData cr get
1 index bitwidth bitheight rowbytes rSmt tso smooth4}
}{rowbytes 3 bitshift bitheight 4 add true
[bitwidth 0 0 bitheight neg 0 bitheight 2 add]
{CharData cr get}
}ifelse
imagemask
}if
}ifelse
restore
end end
}bdf
/bb{.96 exch div/Gnormsize mdf 2 index
/Gkernmax mdf 1 index/Gdescent mdf
3 index div 4 1 roll
2 index div 1. 5 2 roll
exch div 4 1 roll
4 array astore/FontBBox mdf
}bdf
/cdf{mfont/CharData get 3 1 roll put}bdf
/bf{
mfont begin
/FontType 3 def
/FontMatrix [1 0 0 1 0 0] def
/Encoding macvec def
/MFontType 0 def
/BuildChar/bmbc load def
end
mfont definefont pop
}bdf
/wi LW 1 eq{{gsave 0 0 0 0 0 0 0 0 moveto lineto lineto lineto closepath clip stringwidth grestore}bind}{/stringwidth load}ifelse def
/aps{0 get 124 eq}bdf
/xc{s75 cvs dup}bdf
/xp{put cvn}bdf
/scs{xc 3 67 put dup 0 95 xp}bdf
/sos{xc 3 79 xp}bdf
/sbs{xc 1 66 xp}bdf
/sis{xc 2 73 xp}bdf
/sob{xc 2 79 xp}bdf
/sss{xc 4 83 xp}bdf
/dd{exch 1 index add 3 1 roll add exch}bdf
/smc{moveto dup show}bdf
/ndf2{udf{dup /FontType get 0 eq{/FDepVector get{dup /FontType get 0 eq{ndf2}{dup /df2 known{begin df2 0 null put end
}{pop}ifelse}ifelse}forall}{/df2 known{dup begin df2 0 null put end}if}ifelse}{pop}ifelse}bdf
/kwn{FontDirectory 1 index known{findfont dup ndf2 exch pop}}bdf
/gl{1 currentgray sub setgray}bdf
/newmm{dup /FontType get 0 eq{dup maxlength dict begin{1 index/FID ne 2 index/UniqueID ne and{def}{pop pop}ifelse}forall currentdict end
dup /FDepVector 2 copy get[exch 6 index exch 6 index exch{newmm 3 1 roll}forall pop pop] put dup
}{/mfont 10 dict def mfont begin/FontMatrix [1 0 0 1 0 0] def
/FontType 3 def/Encoding macvec def/df 1 index def/df2 1 array def/FontBBox [0 0 1 1] def/StyleCode 2 index def
/mbc{bcarray StyleCode get}def/BuildChar{exch begin	wd begin/cr exch def/cs s1 dup 0 cr put def df /MFontType known not{
df2 0 get null eq{df dup length 2 add dict begin{1 index/FID ne 2 index/UniqueID ne and{def}{pop pop}ifelse}forall
/StrokeWidth nlw 1000 mul pys div ps div dup 12 lt{pop 12}if def/PaintType 2 def currentdict end
/q exch definefont df2 exch 0 exch put}if}if mbc exec end end}def end mfont}ifelse
3 index exch definefont exch pop}bdf
/mb{dup sbs kwn{0 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
/mo{dup sos kwn{2 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
/ms{dup sss kwn{4 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
/ou{dup sos kwn{mfont/df2 known{mfont begin df2 0 null put end}if 3 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
/su{dup sss kwn{mfont/df2 known{mfont begin df2 0 null put end}if 5 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
/ao{/fmv true def ou}bdf/as{/fmv true def su}bdf
/vo{/fmv false def ou}bdf/vs{/fmv false def su}bdf
/c{currentrgbcolor dup 4 1 roll eq 3 1 roll eq and/gray xdf}bdf
/bcarray[{/da .03 def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth
cs 0 0 smc da 0 smc da da smc 0 da moveto show}bind dup{/da 1 ps div def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth
cs 0 0 smc da 0 smc da da smc 0 da smc c gray{gl}{1 setgray}ifelse da 2. div dup moveto show}bind
{df setfont gsave cs wi grestore setcharwidth c gray{gl}{currentrgbcolor 1 setgray}ifelse cs 0 0 smc df2 0 get setfont
gray{gl}{4 1 roll setrgbcolor}ifelse 0 0 moveto show}bind
{/da 1 ps div def/ds .05 def/da2 da 2. div def df setfont gsave cs wi 1 index 0 ne{exch ds add da2 add exch}if grestore setcharwidth
cs ds da2 add .01 add 0 smc 0 ds da2 sub translate 0 0 smc da 0 smc da da smc 0 da smc c gray{gl}{1 setgray}ifelse da 2. div dup moveto show}bind
{/da .05 def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth c cs da .01 add 0 smc 0 da translate
gray{gl}{currentrgbcolor 1 setgray 4 -1 roll}ifelse 0 0 smc gray{gl}{4 1 roll setrgbcolor}ifelse df2 0 get setfont 0 0 moveto show}bind]def
/st{1000 mul usertime add dup 2147483647 gt{2147483647 sub}if def}bdf
/the{usertime sub dup 0 lt exch -2147483648 gt and}bdf
/6a 6 array def
/2a 2 array def
/3q 3 array def
/qs{3 -1 roll sub exch 3 -1 roll sub exch}bdf
/qa{3 -1 roll add exch 3 -1 roll add exch}bdf
/qm{3 -1 roll 1 index mul 3 1 roll mul}bdf
/qn{6a exch get mul}bdf
/qA .166667 def/qB .833333 def/qC .5 def
/qx{6a astore pop
qA 0 qn qB 2 qn add   qA 1 qn qB 3 qn add
qB 2 qn qA 4 qn add   qB 3 qn qA 5 qn add
qC 2 qn qC 4 qn add   qC 3 qn qC 5 qn add}bdf
/qp{6 copy 12 -2 roll pop pop}bdf
/qc{exch qp qx curveto}bdf
/qi{{exch 4 copy 2a astore aload pop qa .5 qm newpath moveto}{exch 2 copy 6 -2 roll 2 qm qs 4 2 roll}ifelse}bdf
/qq{{qc 2a aload pop qx curveto}{exch 4 copy qs qa qx curveto}ifelse}bdf
/pt{currentpoint newpath moveto}bdf
/qf{/fillflag true def}bdf
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%%Title: GDE2.0_small
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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
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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
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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
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753 90 gm
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0 gr
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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
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0 0 gm
(nc 72 90 269 544 6 rc)kp
64 gr
112 136 243 419 1 rc
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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
T 248 15.90908 163 295 70 554 35 T 1 db
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48 gr
391.5 255.5 446.5 314.5 90 180 0 ar
391.5 255.5 446.5 314.5 0 90 0 ar
0 0 2 9 9 2 dh
419 314 gm
425 321 lin
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
T 134 33.87997 235 297 40 305 77 T 1 db
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(nc 31 30 761 582 6 rc)kp
0 gr
T 1 setTxMode
12 fz
2 F /|______Times-Roman fnt
0.15495 0.(Protections...)ashow
485 90 gm
10 fz
2 F /|______Times-Roman fnt
-0.01272 0.(This will display, and then set the default protections for all selected sequences.  If two or more of the)ashow
496 90 gm
-0.02812 0.(sequences differ in their current protection settings, a warning message will appear in the protection dialog)ashow
507 90 gm
-0.00859 0.(box.  The protections currently available are alignment gap protection, ambiguous character protection,)ashow
518 90 gm
-0.02893 0.(unambiguous character protection, and translation protection.)ashow
0 0 gm
(nc 520 270 600 352 6 rc)kp
64 gr
521 271 599 351 1 rc
0 gr
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285 90 gm
(nc 31 30 761 582 6 rc)kp
0 gr
T 1 setTxMode
14 fz
2 F /|______Times-Roman fnt
0.53985 0. 32 0.05398 0.( Edit menu)awidthshow
308 90 gm
12 fz
2 F /|______Times-Roman fnt
-0.29429 0.(Select All)ashow
320 90 gm
10 fz
2 F /|______Times-Roman fnt
-0.03724 0.(Selects all sequences.  This is helpful when you have several dozen sequences.)ashow
342 90 gm
12 fz
2 F /|______Times-Roman fnt
0.19332 0. 32 0.01933 0.(Select by name...)awidthshow
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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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
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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
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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
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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
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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
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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
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%%EOF