menu:File item:test cmask output itemmethod: textedit in1 in:in1 informat:colormask item:New sequence itemmethod:echo "$Type$Name" > out1 itemmeta:n itemhelp:new_sequence.help arg:Name argtype:text arglabel:New Sequence name? argtext:New arg:Type argtype:choice_list arglabel:Type? argchoice:DNA/RNA:# argchoice:Amino Acid:% argchoice:Text:\" argchoice:Mask:@ out:out1 outformat:flat item:Import Foreign Format itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp itemhelp:readseq.help arg:INPUTFILE argtype:text arglabel:Name of foreign file? out:OUTPUTFILE outformat:genbank item:Export Foreign Format itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE itemhelp:readseq.help arg:FORMAT argtype:choice_list argchoice:IG/Stanford:1 argchoice:GenBank:2 argchoice:NBRF:3 argchoice:EMBL:4 argchoice:GCG:5 argchoice:DNA Strider:6 argchoice:Fitch:7 argchoice:Pearson:8 argchoice:Zuker:9 argchoice:Olsen:10 argchoice:Phylip v3.2:11 argchoice:Phylip v3.3:12 argchoice:Plain text:13 arg:OUTPUTFILE argtype:text arglabel:Save as? in:INPUTFILE informat:genbank item:Save Selection itemmethod: cat $SAVE_FUNC > $Name itemhelp:save_selection.help arg:SAVE_FUNC argtype:chooser arglabel:File format argchoice:Flat:in1 argchoice:Genbank:in2 argchoice:GDE/HGL:in3 arg:Name argtype:text arglabel:File name? in:in1 informat:flat in:in2 informat:genbank in:in3 informat:gde item:Print Selection itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)& itemhelp:print_alignment.help arg:SCALE argtype:slider arglabel:Reduce printout by? argmin:1 argmax:20 argvalue:1 arg:CMD argtype:chooser argchoice:Lpr:lpr argchoice:Enscript Gaudy:enscript -G -q argchoice:Enscript Two column:enscript -2rG arg:PRINTER argtype:text arglabel:Which printer? argtext:lp in:in1 informat:gde insave: menu:Edit item:Sort itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)& itemhelp:heapsortHGL.help arg:PRIM_KEY argtype:choice_list argchoice:Group:group-ID argchoice:type:type argchoice:name:name argchoice:Sequence ID:sequence-ID argchoice:creator:creator argchoice:offset:offset arglabel:Primary sort field? arg:SEC_KEY argtype:choice_list argchoice:None: argchoice:Group:group-ID argchoice:type:type argchoice:name:name argchoice:Sequence ID:sequence-ID argchoice:creator:creator argchoice:offset:offset arglabel:Secondary sort field? in:in1 informat:gde insave: item:extract itemmethod:(gde in1;/bin/rm -f in1)& in:in1 informat:gde inmask: insave: menu:DNA/RNA item:Translate... itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1 arg:FRAME argtype:chooser arglabel:Which reading frame? argchoice:First:1 argchoice:Second:2 argchoice:Third:3 argchoice:All six:6 arg:MNFRM arglabel:Minimum length of AA sequence to translate? argtype:slider argmin:0 argmax:100 argvalue:20 arg:LTRCODE argtype:chooser arglabel:Translate to: argchoice:Single letter codes: argchoice:Triple letter codes:-3 arg:TBL arglabel:Codon table? argtype:chooser argchoice:universal:1 argchoice:mycoplasma:2 argchoice:yeast:3 argchoice:Vert. mito.:4 in:in1 informat:gde out:out1 outformat:gde item:Dot plot itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)& itemhelp:DotPlotTool.help in:in1 informat:gde insave: item:Clustal alignment itemmethod:(tr '%#' '>'clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1* )& itemhelp:clustal_help arg:KTUP argtype:slider arglabel:K-tuple size for pairwise search argmin:1 argmax:10 argvalue:2 arg:WIN argtype:slider arglabel:Window size argmin:1 argmax:10 argvalue:4 arg:Trans argtype:chooser arglabel:Transitions weighted? argchoice:Yes:/TRANSIT argchoice:No: arg:FIXED argtype:slider arglabel:Fixed gap penalty argmin:1 argmax:100 argvalue:10 arg:FLOAT arglabel:Floating gap penalty argtype:slider argmin:1 argmax:100 argvalue:10 arg:REPORT argtype:chooser arglabel:View assembly report? argchoice:No: argchoice:Yes:textedit in1.rpt& in:in1 informat:flat insave: item:Variable Positions itemmethod:varpos $REV < in1 > out1 arg:REV argtype:chooser arglabel:Highlight (darken) argchoice:Conserved positions: argchoice:variable positions:-rev in:in1 informat:flat out:out1 outformat:colormask item:Phrap itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*; in:in1 informat:genbank out:out1 outformat:genbank item:Find all itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1; itemhelp:findall.help itemmeta:f arg:SEARCH argtype:text arglabel:Search String arg:PRCNT argtype:slider arglabel:Percent mismatch argmin:0 argmax:75 argvalue:10 arg:CASE argtype:chooser arglabel:Case argchoice:Upper equals lower: argchoice:Upper not equal lower:-case arg:UT argtype:chooser arglabel:U equal T? argchoice:Yes:-u=t argchoice:No: argvalue:0 arg:MAT arglabel:Match color argtype:choice_list argchoice:yellow:1 argchoice:violet:2 argchoice:red:3 argchoice:aqua:4 argchoice:green:5 argchoice:blue:6 argchoice:grey:11 argchoice:black:8 argvalue:2 arg:MIS argtype:choice_list arglabel:Mismatch color argchoice:yellow:1 argchoice:violet:2 argchoice:red:3 argchoice:aqua:4 argchoice:green:5 argchoice:blue:6 argchoice:grey:11 argchoice:black:8 argvalue:7 in:in1 informat:flat out:out1 outformat:colormask item:Sequence Consensus itemmethod:(MakeCons in1 $METHOD $MASK > out1) itemhelp:MakeCons.help arg:METHOD arglabel:Method argtype:chooser argchoice:IUPAC:-iupac argchoice:Majority:-majority $PERCENT arg:MASK argtype:chooser arglabel:Create a new: argchoice:Sequence: argchoice:Selection Mask: | Consto01mask arg:PERCENT arglabel:Minimum Percentage for Majority argtype:slider argmin:50 argmax:100 argvalue:75 in:in1 informat:gde out:out1 outformat:gde item:MFOLD itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)& itemhelp:MFOLD.help in:seqGB informat:genbank insave: arg:METHOD argtype:chooser arglabel:RNA type argchoice:Fold Linear RNA:lrna argchoice:Fold Circular RNA:crna arg:CT argtype:text arglabel:Pairing(ct) File Name argtext:mfold_out item:Draw Secondary structure itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) & itemhelp:LoopTool.help arg:TEMPLATE argtype:chooser arglabel:Use template file ./loop.temp? argchoice:No: argchoice:Yes:-t loop.temp in:in1 informat:genbank insave: item:Highlight helix itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat itemhelp:sho_helix.help in:in1 informat:genbank out:out1 outformat:colormask #Menu for DNA/RNA item:blastn itemmethod:(sed "s/[#%]/>/" in1.f; /usr/local/biotools/blast/blastall -p blastn -d $BLASTDB -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1*)& in:in1 informat:flat insave: arg:BLASTDB argtype:choice_list arglabel:Which Database argchoice:Genome HIV position:/var/www/cgi-bin/db/genomeHIV.fasta argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate argchoice:HIV-1:/var/www/cgi-bin/db/hivallsequencesGB-31-10.fasta argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta argchoice:HIV-1 HXB2 Numb:/var/www/cgi-bin/db/HXB2.fasta argchoice:HIV-1 HXB2 Numb:/var/www/cgi-bin/db/HXB2.fasta arg:WORDLEN argtype:slider arglabel:Word Size argmin:4 argmax:18 argvalue:12 arg:MATCH argtype:slider arglabel:Match Score argmin:1 argmax:10 argvalue:5 arg:MMSCORE argtype:slider arglabel:Mismatch Score argmin:-10 argmax:-1 argvalue:-5 item:blastx itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: arg:BLASTDB argtype:choice_list arglabel:Which Database argchoice:pir1:$GDE_HELP_DIR/BLAST/pir argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept arg:WORDLEN argtype:slider arglabel:Word Size argmin:1 argmax:5 argvalue:3 arg:Matrix arglabel:Substitution Matrix: argtype:choice_list argchoice:PAM120:PAM120 argchoice:PAM250:PAM250 arg:CODE argtype:choice_list arglabel:Genetic Code argchoice:Standard or Universal:0 argchoice:Vertebrate Mitochondrial:1 argchoice:Yeast Mitochondrial:2 argchoice:Mold Mitochondrial and Mycoplasma:3 argchoice:Invertebrate Mitochondrial:4 argchoice:Ciliate Macronuclear:5 argchoice:Protozoan Mitochondrial:6 argchoice:Plant Mitochondrial:7 argchoice:Echinodermate Mitochondrial:8 item:FASTA (DNA/RNA) itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & itemhelp:FASTA.help in:in1 informat:flat arg:DBASE argtype:choice_list arglabel:Database argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1 argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1 argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1 argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1 argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1 argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1 argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1 argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1 argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1 argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1 argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1 argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1 argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1 arg:NUMOFALN argtype:slider arglabel:Number of Alignment to Report argmin:1 argmax:100 argvalue:20 arg:MATRIX arglabel:Which SMATRIX argtype:choice_list argchoice:Default: argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat menu:DB item:DB X8873 itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp itemhelp:readseq.help arg:INPUTFILE argtype:chooser arglabel:Databases argchoice:subtype:/home/database/DNA/subtyperef/subcomplete.fasta argchoice:SIVENVDNA.fasta:/home/database/DNA/SIVENVDNA.fasta out:OUTPUTFILE outformat:genbank item:HIV-1 Subtype itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp itemhelp:readseq.help arg:INPUTFILE argtype:choice_list arglabel:HIV-1 Subtype genome regions argchoice:CG:/home/database/DNA/subtyperef/subcomplete.fasta argchoice:sub5ltr.fasta:/home/database/DNA/subtyperef/sub5ltr.fasta argchoice:sub5ltrU3.fasta:/home/database/DNA/subtyperef/sub5ltrU3.fasta argchoice:sub5ltrU5.fasta:/home/database/DNA/subtyperef/sub5ltrU5.fasta argchoice:subenv.fasta:/home/database/DNA/subtyperef/subenv.fasta argchoice:subenv-gp120.fasta:/home/database/DNA/subtyperef/subenv-gp120.fasta argchoice:subenv-gp41.fasta:/home/database/DNA/subtyperef/subenv-gp41.fasta argchoice:subenvv3.fasta:/home/database/DNA/subtyperef/subenvv3.fasta argchoice:subgag.fasta:/home/database/DNA/subtyperef/subgag.fasta argchoice:subgag-p17.fasta:/home/database/DNA/subtyperef/subgag-p17.fasta argchoice:subgag-p24.fasta:/home/database/DNA/subtyperef/subgag-p24.fasta argchoice:subgag-pol.fasta:/home/database/DNA/subtyperef/subgag-pol.fasta argchoice:subpol.fasta:/home/database/DNA/subtyperef/subpol.fasta argchoice:subpol-p15RNAase.fasta:/home/database/DNA/subtyperef/subpol-p15RNAase.fasta argchoice:subpol-p31integrase.fasta:/home/database/DNA/subtyperef/subpol-p31integrase.fasta argchoice:subpol-p51RT.fasta:/home/database/DNA/subtyperef/subpol-p51RT.fasta argchoice:subpol-protease.fasta:/home/database/DNA/subtyperef/subpol-protease.fasta argchoice:subrevCDS.fasta:/home/database/DNA/subtyperef/subrevCDS.fasta argchoice:subrevexon1.fasta:/home/database/DNA/subtyperef/subrevexon1.fasta argchoice:subrevexon2.fasta:/home/database/DNA/subtyperef/subrevexon2.fasta argchoice:subrevintron.fasta:/home/database/DNA/subtyperef/subrevintron.fasta argchoice:subTAR.fasta:/home/database/DNA/subtyperef/subTAR.fasta argchoice:subtatCDS.fasta:/home/database/DNA/subtyperef/subtatCDS.fasta argchoice:subtatexon1.fasta:/home/database/DNA/subtyperef/subtatexon1.fasta argchoice:subtatexon2.fasta:/home/database/DNA/subtyperef/subtatexon2.fasta argchoice:subtatintron.fasta:/home/database/DNA/subtyperef/subtatintron.fasta argchoice:subvif.fasta:/home/database/DNA/subtyperef/subvif.fasta argchoice:subvpr.fasta:/home/database/DNA/subtyperef/subvpr.fasta argchoice:subvpu.fasta:/home/database/DNA/subtyperef/subvpu.fasta argchoice:subnef.fasta:/home/database/DNA/subtyperef/subnef.fasta out:OUTPUTFILE outformat:genbank item:HXB2 itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp itemhelp:readseq.help arg:INPUTFILE argtype:chooser arglabel:HXB2 Reference Seq argchoice:CG:/home/database/DNA/HXB2.fasta out:OUTPUTFILE outformat:genbank menu:Protein item:Clustal Protein Alignment itemmethod:(tr '%#"' '>' clus_in;clustalw /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* gde* )& itemhelp:clustal_help arg:KTUP argtype:slider arglabel:K-tuple size for pairwise search argmin:1 argmax:10 argvalue:2 arg:WIN argtype:slider arglabel:Window size argmin:1 argmax:10 argvalue:4 arg:Matrx argtype:chooser arglabel:Weighting matrix argchoice:PAM 250:PAM250 argchoice:PAM 100:PAM100 argchoice:Identity:ID arg:FIXED argtype:slider arglabel:Fixed gap penalty argmin:1 argmax:100 argvalue:10 arg:FLOAT arglabel:Floating gap penalty argtype:slider argmin:1 argmax:100 argvalue:10 arg:REPORT argtype:chooser arglabel:View assembly report? argchoice:No: argchoice:Yes:textedit in1.rpt& in:in1 informat:flat insave: #Menu for Protein item:blastp itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: arg:BLASTDB argtype:choice_list arglabel:Which Database argchoice:pir:$GDE_HELP_DIR/BLAST/pir argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept argchoice:local:$GDE_HELP_DIR/BLAST/local_db arg:Matrix arglabel:Substitution Matrix: argtype:choice_list argchoice:PAM120:PAM120 argchoice:PAM250:PAM250 arg:WORDLEN argtype:slider arglabel:Word Size argmin:1 argmax:5 argvalue:3 item:tblastn itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: arg:BLASTDB argtype:choice_list arglabel:Which Database argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate arg:Matrix arglabel:Substitution Matrix: argtype:choice_list argchoice:PAM120:PAM120 argchoice:PAM250:PAM250 arg:WORDLEN argtype:slider arglabel:Word Size argmin:4 argmax:18 argvalue:12 arg:CODE argtype:choice_list arglabel:Genetic Code argchoice:Standard or Universal:0 argchoice:Vertebrate Mitochondrial:1 argchoice:Yeast Mitochondrial:2 argchoice:Mold Mitochondrial and Mycoplasma:3 argchoice:Invertebrate Mitochondrial:4 argchoice:Ciliate Macronuclear:5 argchoice:Protozoan Mitochondrial:6 argchoice:Plant Mitochondrial:7 argchoice:Echinodermate Mitochondrial:8 item:blast3 itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: arg:BLASTDB argtype:choice_list arglabel:Which Database argchoice:pir1:$GDE_HELP_DIR/BLAST/pir argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept arg:Matrix arglabel:Substitution Matrix: argtype:choice_list argchoice:PAM120:PAM120 argchoice:PAM250:PAM250 arg:WORDLEN argtype:slider arglabel:Word Size argmin:1 argmax:5 argvalue:3 item:FASTA (Protein) itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & itemhelp:FASTA.help in:in1 informat:flat arg:DBASE argtype:choice_list arglabel:Database argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2 argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2 argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2 arg:NUMOFALN argtype:slider arglabel:Number of Alignment to Report argmin:1 argmax:100 argvalue:20 arg:MATRIX arglabel:Which SMATRIX argtype:choice_list argchoice:Default: argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat menu:Seq management item:Assemble Contigs itemmethod:(sed "s/#/>/"in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp) itemhelp:CAP2.help arg:OVERLAP argtype:slider arglabel:Minimum overlap? argmin:5 argmax:100 argvalue:20 arg:PMATCH argtype:slider arglabel:Percent match required within overlap argmin:25 argmax:100 argvalue:90 in:in1 informat:flat out:out1 outformat:gde outoverwrite: item:Map View itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)& itemhelp:mapview.help in:in1 informat:gde insave: arg:PBL arglabel:Pixel Between Lines argtype:slider argvalue:10 argmin:1 argmax:15 arg:NPP arglabel:Nucleotides Per Pixel argtype:slider argvalue:1 argmin:1 argmax:20 arg:LWIDTH arglabel:Line Thickness argtype:slider argvalue:2 argmin:1 argmax:5 item:Restriction sites itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp); itemhelp:Restriction.help arg:ENZ argtype:text arglabel:Enzyme file argtext:$GDE_HELP_DIR/DATA_FILES/enzymes arg:PRE_EDIT argtype:chooser arglabel:Edit enzyme file first? argchoice:Yes:textedit in1.tmp; argchoice:No: in:in1 informat:flat out:out1 outformat:colormask menu:Phylogeny item:DeSoete Tree fit itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )& itemhelp:lsadt.help in:in1 informat:genbank insave: inmask: arg:CORR arglabel:Distance correction? argtype:chooser argchoice:Olsen:-c=olsen argchoice:Jukes/Cantor:-c=jukes argchoice:None:-c=none arg:INIT arglabel:Initial parameter estimate argtype:choice_list argchoice:uniformly distributed random numbers:1 argchoice:error-perturbed data:2 argchoice:original distance data from input matrix:3 arg:SEED argtype:slider arglabel:Random number seed argmin:0 argmax:65535 argvalue:12345 arg:DISPLAY_FUNC argtype:chooser arglabel:View tree using argchoice:TextEdit:textedit argchoice:Treetool:treetool < item:Phylip help itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)& arg:FILE argtype:choice_list arglabel:Which program? argchoice:boot:boot.doc argchoice:clique:clique.doc argchoice:consense:consense.doc argchoice:contchar:contchar.doc argchoice:contml:contml.doc argchoice:contrast:contrast.doc argchoice:discrete:discrete.doc argchoice:distance:distance.doc argchoice:dnaboot:dnaboot.doc argchoice:dnacomp:dnacomp.doc argchoice:dnadist:dnadist.doc argchoice:dnainvar:dnainvar.doc argchoice:dnaml:dnaml.doc argchoice:dnamlk:dnamlk.doc argchoice:dnamove:dnamove.doc argchoice:dnapars:dnapars.doc argchoice:dnapenny:dnapenny.doc argchoice:dolboot:dolboot.doc argchoice:dollop:dollop.doc argchoice:dolmove:dolmove.doc argchoice:dolpenny:dolpenny.doc argchoice:draw:draw.doc argchoice:drawgram:drawgram.doc argchoice:drawtree:drawtree.doc argchoice:factor:factor.doc argchoice:fitch:fitch.doc argchoice:gendist:gendist.doc argchoice:kitsch:kitsch.doc argchoice:main:main.doc argchoice:mix:mix.doc argchoice:move:move.doc argchoice:neighbor:neighbor.doc argchoice:penny:penny.doc argchoice:protpars:protpars.doc argchoice:read.me.general:read.me.general.doc argchoice:restml:restml.doc argchoice:seqboot:seqboot.doc argchoice:sequence:sequence.doc item:Phylip 3.4 itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )& arg:PROGRAM argtype:choice_list arglabel:Which program to run? argchoice:DNAPARS:dnapars argchoice:DNABOOT:dnaboot argchoice:DNAPENNY:dnapenny argchoice:DNAML:dnaml argchoice:DNAMLK:dnamlk argchoice:DNACOMP:dnacomp argchoice:DNAMOVE:dnamove argchoice:DNAINVAR:dnainvar argchoice:PROTPARS:protpars arg:PREEDIT argtype:chooser arglabel:Edit input before running? argchoice:No: argchoice:Yes:textedit infile; in:in1 informat:genbank inmask: insave: item:Phylip Distance methods itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ; $PREEDIT shelltool seqboot; mv -f outfile infile; shelltool dnadist;mv -f outfile infile; shelltool neighbor; cp outtree intree; $PROGRAM textedit outfile;/bin/rm -f in1 infile outfile)& arg:PROGRAM arglabel:Which method? argtype:chooser argchoice:DNADIST:mv -f infile outfile; argchoice:Fitch:shelltool fitch; argchoice:Kitsch:shelltool kitsch; argchoice:Neighbor:shelltool neighbor; argchoice:Full:shelltool consense; arg:PREEDIT argtype:chooser arglabel:Edit input before running? argchoice:No: argchoice:Yes:textedit infile; in:in1 informat:genbank inmask: insave: menu:W item:Stanford itemmethod:(readseq in1 -a -f8 > infile.fasta; netscape http://hiv-4.stanford.edu/cgi-bin/hivseqweb.pl?uploaded_file=infile.fasta)& in:in1 informat:genbank item:Los Alamos DB Search itemmethod:(netscape http://hiv-web.lanl.gov/cgi-bin/hivDB3/public/wdb/ssampublic)& item:Retroviruses NCBI itemmethod:(netscape http://www.ncbi.nlm.nih.gov/retroviruses/)& item:SNAP (sy/nosy)& itemmethod:(netscape http://hiv-web.lanl.gov/SNAP/WEBSNAP/SNAP.html)& item:PubMed itemmethod:(netscape http://www.ncbi.nlm.nih.gov/Entrez/) in:in1 informat:genbank menu:Email item:BLASTN itemmethod:(echo BLASTPROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo MATCH $MSCORE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & arg:DBASE argtype:choice_list arglabel:Which Database? argchoice:GenBank Qtrly & Updates:GenBank argchoice:EMBL:embl arg:MSCORE argtype:slider arglabel:Match Score argmin:3 argmax:7 argvalue:5 in:in1 informat:flat insave: item:BLASTP itemmethod:(echo BLASTPROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & arg:DBASE argtype:choice_list arglabel:Which Database? argchoice:Swiss-Prot:swiss-prot argchoice:PIR:pir in:in1 informat:flat insave: item:Fasta-(DNA) itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $KPL >> in1.tmp; echo SCORES $TOP >> in1.tmp; echo ALIGNMENTS $ALNG >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & arg:DBASE argtype:choice_list arglabel:Which GenBank Database? argchoice:Qrtly & Updates:GenBank/all argchoice:Updates:GenBank/new argchoice:Primate:GenBank/primate argchoice:Rodent:GenBank/rodent argchoice:Other-Mammalian:GenBank/other_mammalian argchoice:Other-Vertebrate:GenBank/other_vertebrate argchoice:Invertebrate:GenBank/invertebrate argchoice:Plant:GenBank/plant argchoice:Organelle:GenBank/organelle argchoice:Bacterial:GenBank/bacterial argchoice:Structural-RNA:GenBank/structural_rna argchoice:Viral:GenBank/viral argchoice:Phage:GenBank/phage argchoice:Synthetic:GenBank/synthetic argchoice:Unannotated:GenBank/unannotated arg:KPL argtype:slider arglabel:K-tuple window argmin:3 argmax:6 argvalue:4 arg:TOP argtype:slider arglabel:Scores Displayed? argmin:1 argmax:200 argvalue:100 arg:ALNG argtype:slider arglabel:# Alignments Displayed? argmin:1 argmax:200 argvalue:20 in:in1 informat:flat insave: item:Fasta-(PROTEIN) itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $TPL >> in1.tmp; echo SCORES $SCRS >> in1.tmp; echo ALIGNMENTS $ALNMNTS >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & arg:DBASE argtype:choice_list arglabel:Which Protein Database? argchoice:Trans GenBank Qrtly:GenPept/all argchoice:Trans GenBank Daily:GenPept/new argchoice:Swiss-Protein:SWISS-PROT/all arg:TPL argtype:slider arglabel:K-TUP window argmin:1 argmax:2 argvalue:1 arg:SCRS argtype:slider arglabel:# Scores Displayed? argmin:1 argmax:200 argvalue:100 arg:ALNMNTS argtype:slider arglabel:# Alignments Displayed? argmin:1 argmax:200 argvalue:20 in:in1 informat:flat insave: item:GeneID itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) & arg:REPRINT argtype:chooser arglabel:Do you want a GENEID reprint? argchoice:YES:echo "Preprint Request" >> in1.tmp argchoice:NO in:in1 informat:flat insave: item:Sequence Retrieval itemmethod:(echo $REGEXP > in1.tmp; Mail RETRIEVE@GENBANK.BIO.NET < in1.tmp; rm in1.tmp) & arg:REGEXP argtype:text arglabel:Accession # or LOCUS name of sequence to retrieve item:Grail itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp) arg:NAME argtype:text arglabel:Your Name arg:ADDRESS argtype:text arglabel:Your Address arg:PHONE argtype:text arglabel:Your Phone Number arg:EMAIL argtype:text arglabel:Your E-Mail Address # # dgg added new readseq formats, 29 dec 92 # item:Export Foreign Format itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE itemhelp:readseq.help arg:FORMAT argtype:choice_list argchoice:GenBank:genbank argchoice:IG/Stanford:ig argchoice:NBRF:nbrf argchoice:EMBL:embl argchoice:GCG:gcg argchoice:DNA Strider:strider argchoice:Fitch:fitch argchoice:Pearson/Fasta:pearson argchoice:Zuker:zuker argchoice:Olsen:olsen argchoice:Phylip:phylip #argchoice:Phylip v3.2:phylip3.2 argchoice:Plain text:raw argchoice:ASN.1:asn argchoice:PIR:pir argchoice:MSF:msf argchoice:PAUP:paup argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop arg:OUTPUTFILE argtype:text arglabel:Save as? in:in1 informat:genbank # #dgg addition for new readseq, 24 dec 92 # item:Pretty Print itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)& itemhelp:readseq.help #nametop is bad !? in:in1 informat:genbank arg:NAMETOP argtype:chooser arglabel:Names at top ? argchoice:No: argchoice:Yes:-nametop arg:NAMELEFT argtype:chooser arglabel:Names at left ? argchoice:No: argchoice:Yes:-nameleft arg:NAMERIGHT argtype:chooser arglabel:Names at right? argchoice:Yes:-nameright argchoice:No: arg:NUMTOP argtype:chooser arglabel:Numbers at top ? argchoice:Yes:-numtop argchoice:No: arg:NUMBOT argtype:chooser arglabel:Numbers at tail ? argchoice:No: argchoice:Yes:-numbot arg:NUMLEFT argtype:chooser arglabel:Numbers at left ? argchoice:Yes:-numleft argchoice:No: arg:NUMRIGHT argtype:chooser arglabel:Numbers at right? argchoice:Yes:-numright argchoice:No: arg:MATCH argtype:chooser arglabel:Use match '.' for 2..n species? argchoice:No: argchoice:Yes:-match arg:GAPC argtype:chooser arglabel:Count gap symbols? argchoice:No: argchoice:Yes:-gap arg:WIDTH argtype:slider arglabel:Sequence width? argmin:10 argmax:200 argvalue:50 arg:COLS argtype:slider arglabel:Column spacers? argmin:0 argmax:50 argvalue:10 ### pretty print insert end # item:Wally's test function itemmethod:run__wally $ONE $TWO $THREE < $FILE arg:ONE argtype:chooser arglabel:How? argchoice:Fast:-fast argchoice:Slow:-slow arg:TWO argtype:slider argmin:0 argmax:100 argvalue:50 arglabel:how many? arg:THREE argtype:choice_list arglabel:Which one? argchoice:Fast:-fast argchoice:Slow:-slow arg:FILE argtype:text arglabel:Which file