GCG GCG_HOME=/usr/local/gcg/ callgcg='/usr/local/gcg/callgcg ' PATH=${GCG_HOME}/gcgbin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin stderr=childapp.stderr stdout=childapp.stdout assemble local: Sequence Edit|Assemble TITLE Assemble (GCG) INFO About Sequence Edit - Assemble (GCG) Main1 Main true 2 output biosequence/gcg output List file of output sequence names -LIStfile Optional2 Optional false 1 Monitor program progress false -MONitor HELP Help for Assemble http://sunflower.bio.indiana.edu/~gcg/genhelp/assemble.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}assemble $2 $1 $INfile $OUTfile backtranslate local: Translation|BackTranslate TITLE BackTranslate (GCG) INFO About Translation - BackTranslate (GCG) Main3 Main true 100 false 10 table of back-translations and most probable sequence false -MENu=A 11 table of back-translations and most ambiguous sequence true -MENu=B 12 most probable sequence only false -MENu=C 13 most ambiguous sequence only false -MENu=D 3 input biosequence/gcg input Codon Frequency Table -INfile2 1 output biosequence/gcg translate.txt output Translation Table -TRANSlate Optional4 Optional false 2 Window size (in number of codons) for probability of\npreferred codons occuring together by chance 4, 1, 15, 1 -WINdow HELP Help for BackTranslate http://sunflower.bio.indiana.edu/~gcg/genhelp/backtranslate.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}backtranslate $100 $10 $100 $11 $100 $12 $100 $13 $100 $3 $1 $2 $INfile1 $OUTfile bestfit local: Pairwise Comparison|BestFit TITLE BestFit (GCG) INFO About Pairwise Comparison - BestFit (GCG) Optional5 Optional false 30 output biosequence/gcg Prot ? blosum62.cmp : swgapdna.cmp output Scoring Matrix -MATRix 3 Set gap creation penalty -GAPweight 4 Set gap extension penalty -LENgthweight 31 Don't penalize gap extensions longer than -PENAlizedlength 20 Gap shift limit for sequence 1 0, 0, 0, 1 -LIMit1 21 Gap shift limit for sequence 2 0, 0, 0, 1 -LIMit2 100 false 10 select "top" alignment for equally optimal alignment (HighRoad) false -MENu=HIGhroad 11 select "bottom" alignment for equally optimal alignment (LowRoad) false -MENu=LOWroad 27982 false Generate statistics from randomized alignments 9,101 -RANdomizations 101 false 102 nucleotide or amino acid composition true 103 dinucleotide or dipeptide composition false -PREServe=2 104 trinucleotide or tripeptide composition false -PREServe=3 9 Number of randomizations 10, 2, 100, 1 -RANdomizations 13 Set thresholds for displaying '|', ':', and '.' (e.g. 4,2,1) -PAIr 12 Number of sequence symbols per line 50, 10, 150, 1 -WIDth 14 Number of lines per page 60, 4, 100, 1 -PAGe 15 true Abbreviate output lines containing only gaps -BIGGaps 6 output biosequence/gcg name(SQ1+.gap) output New sequence file for sequence 1 with gaps added -OUTfile2 7 output biosequence/gcg name(SQ2+.gap) output New sequence file for sequence 2 with gaps added -OUTfile3 18 Include the summary at the end of the program false -SUMmary HELP Help for BestFit http://sunflower.bio.indiana.edu/~gcg/genhelp/bestfit.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 2 ${callgcg}bestfit $30 $3 $4 $31 $20 $21 $100 $10 $100 $11 $100 $27982 $101 $101 $103 $101 $104 $101 $9 $13 $12 $14 $15 $6 $7 $18 $INfile1 $INfile2 $OUTfile1 blast local: Database|Sequence Search|Blast TITLE Blast (GCG) INFO About Database - Sequence Search - Blast (GCG) globalrules +50 35,-50 Main6 Main true 100 false 8 Search a protein database false @1,@9,@71 -MENu=DBProteinonly 9 Search a nucleotide database true @1,81,83,+60,Prot?-71:(#8?-71:+71) -MENu=DBNucleotideonly Optional7 Optional false 40 Filter input sequences for low complexity regions true -FILter 1000 Specify protein scoring matrix false +1010 1010 false 1001 BLOSUM45 false -MATRix=BLOSUM45 1002 BLOSUM62 true -MATRix=BLOSUM62 1003 BLOSUM80 false -MATRix=BLOSUM80 1004 PAM70 false -MATRix=PAM70 1005 PAM30 false -MATRix=PAM30 71 Translate nucleotide sequences false Prot?!72:(#8?!72:(#71?!72:72)),Prot?!73:(#8?!73:(#71?!73:73)) -TBLASTX 72 Reward for all nucleotide matches 1, 1, 5, 1 -MATch 73 Penalty for all nucleotide mismatches -3, -10, -1, 1 -MISmatch 50 false 51 Standard or Universal true -TRANSlate=1 52 Vertebrate Mitochondrial false -TRANSlate=2 53 Yeast Mitochondrial false -TRANSlate=3 54 Mold Mitochondrial and Mycoplasma false -TRANSlate=4 55 Invertebrate Mitochondrial false -TRANSlate=5 56 Ciliate Macronuclear false -TRANSlate=6 57 Echinodermate Mitochondrial false -TRANSlate=9 58 Alternative Ciliate Macronuclear false -TRANSlate=10 59 Eubacterial false -TRANSlate=11 501 Alternative Yeast false -TRANSlate=12 502 Ascidian Mitochondrial false -TRANSlate=13 503 Flatworm Mitochondrial false -TRANSlate=14 504 Blepharisma (ciliate) nuclear false -TRANSlate=15 505 Chlorophycean Mitochondrial false -TRANSlate=16 506 Trematode Mitochondrial false -TRANSlate=21 507 Scenedesmus obliquus Mitochondrial false -TRANSlate=22 508 Thraustochytrium Mitochondrial false -TRANSlate=23 60 false 61 Standard or Universal true -DBTRANSlate=1 62 Vertebrate Mitochondrial false -DBTRANSlate=2 63 Yeast Mitochondrial false -DBTRANSlate=3 64 Mold Mitochondrial and Mycoplasma false -DBTRANSlate=4 65 Invertebrate Mitochondrial false -DBTRANSlate=5 66 Ciliate Macronuclear false -DBTRANSlate=6 67 Echinodermate Mitochondrial false -DBTRANSlate=9 68 Alternative Ciliate Macronuclear false -DBTRANSlate=10 69 Eubacterial false -DBTRANSlate=11 601 Alternative Yeast false -DBTRANSlate=12 602 Ascidian Mitochondrial false -DBTRANSlate=13 603 Flatworm Mitochondrial false -DBTRANSlate=14 604 Blepharisma (ciliate) nuclear false -DBTRANSlate=15 605 Chlorophycean Mitochondrial false -DBTRANSlate=16 606 Trematode Mitochondrial false -DBTRANSlate=21 607 Scenedesmus obliquus Mitochondrial false -DBTRANSlate=22 608 Thraustochytrium Mitochondrial false -DBTRANSlate=23 10 Set non-default word size false @2,+2 2 Word size Prot ? 3: (#8? 3: 11), Prot? 2 : (#8? 2 : 7), Prot? 3 : (#8? 3 : 19), 1 -WORdsize 2400 true Create gapped alignments 2401,2402 -GAPS 2401 Gap creation penalty (Zero selects default) 0, 0, 50, 0 -GAPweight 2402 Gap extension penalty (Zero selects default) 0, 0, 50, 0 -LENgthweight 20 Maximum number of sequence listed in the output @37 500, 1, 1000, 1 -LIStsize 37 Display alignments from how many sequences 250, 1, 0, 1 -ALIgnments 2414 Generate output in native format false !2413 -NATive 2413 Save begin/end attributes in the result file true -FRAgments 34 Pass this string through to the BLAST command line -APPend HELP Help for Blast http://sunflower.bio.indiana.edu/~gcg/genhelp/blast.html IOFiles Input/Output files false INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}blast $100 $8 $100 $9 $100 $40 $1010 $1001 $1010 $1002 $1010 $1003 $1010 $1004 $1010 $1005 $1010 $71 $72 $73 $50 $51 $50 $52 $50 $53 $50 $54 $50 $55 $50 $56 $50 $57 $50 $58 $50 $59 $50 $501 $50 $502 $50 $503 $50 $504 $50 $505 $50 $506 $50 $507 $50 $508 $50 $60 $61 $60 $62 $60 $63 $60 $64 $60 $65 $60 $66 $60 $67 $60 $68 $60 $69 $60 $601 $60 $602 $60 $603 $60 $604 $60 $605 $60 $606 $60 $607 $60 $608 $60 $2 $2400 $2401 $2402 $20 $37 $2414 $2413 $34 $INfile2 $OUTfile chopup local: Utilities|Miscellaneous Utilities|ChopUp TITLE ChopUp (GCG) INFO About Utilities - Miscellaneous Utilities - ChopUp (GCG) Main8 Main true 0 Long file to split input biosequence/gcg input -INfile Optional9 Optional false 2 Maximum line length 50, 10, 200, 5 -LENgth 3 Show the screen monitor of program progress false -MONitor HELP Help for ChopUp http://sunflower.bio.indiana.edu/~gcg/genhelp/chopup.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}chopup $0 $2 $3 $OUTfile circles local: Uncataloged|circles TITLE circles (GCG) INFO About Uncataloged - circles (GCG) Main10 Main true 20 Connect File input biosequence/gcg input -INfile 1 Radius of circle (in platen units) 45.0, 5.0, 45.0, .1 -RADius Optional11 Optional false 100 Set degrees of arc given to each base -ANGleperbase 5 Connect paired bases with chords instead of circles false -CHOrds 2 Display the sequence around the edge false -SHOwseq 4 Draw ticks true 3 -TICks 3 Number the ticks true 200 -NUMbering 200 Set the tick number interval -NUMbering HELP Help for circles http://sunflower.bio.indiana.edu/~gcg/genhelp/circles.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}circles $20 $1 $100 $5 $2 $4 $3 $200 $INfile1 codonfrequency local: Nucleic|Gene Finding|CodonFrequency TITLE CodonFrequency (GCG) INFO About Nucleic - Gene Finding - CodonFrequency (GCG) Optional12 Optional false 1 Input file of codon frequencies input biosequence/gcg input !SQ1 -CODonfile 2 Treat all input sequences as contiguous exons of the same sequence false -ONEPEPtide 3 makes CODONFREQUENCY continue after you write out the file false -CONtinue 4 Show the screen monitor of input sequence names false -MONitor HELP Help for CodonFrequency http://sunflower.bio.indiana.edu/~gcg/genhelp/codonfrequency.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}codonfrequency $1 $2 $3 $4 $INfile $OUTfile1 codonpreference local: Nucleic|Gene Finding|CodonPreference TITLE CodonPreference (GCG) INFO About Nucleic - Gene Finding - CodonPreference (GCG) Main13 Main true 0 output biosequence/gcg ecohigh.cod output Codon Frequency Table -FREQuency 1 Number of codons in window to calculate codon preference curves 25, 1, 500, 1 -PWINdow 2 Rare codon display threshold 0.1, 0.0, 500.0, .1 -RARe Optional14 Optional false 4 output biosequence/gcg translate.txt output Translation Table -TRANSlate 9 output biosequence/gcg name(SQ1+.dat) output Create a table of the codon preference values -FILe 10 output biosequence/gcg name(SQ1+.tab) output Create a table of the statistics for each codon -TABle 13 Do the plot true 5,7,12,14,15,22,9998 -PLOt 7 Show codon preference curves true 16 -PREFerence 22 Show third position bias curves true 6,8,17 -BIAS 6 GC Calculate third position bias for the nucleotide(s) -BIAS 8 Bias window in codons 25, 1, 500, 1 -BWINdow 12 Display open reading frames on the plot true 11 -FRAmes 11 Show all start and stop signals, not just open frames false -ALLFrames 14 Height of the vertical axis (in platen units) 77.0, 5.0, 100.0, 1.0 -PHEIght 15 Length of the horizontal axis (in platen units) 120.0, 5.0, 150.0, 1.0 -PLENgth 16 Maximum value on the codon preference scale 2.2, 0.2, 20.0, 0.1 -PSCAlemax 17 Maximum value on the third position bias scale 1.1, 0.2, 20.0, 0.1 -BSCAlemax 5 output biosequence/gcg output Mark File -MARk 9998 Set the plot density false 9999 9999 Number of bases per centimeter -DENsity HELP Help for CodonPreference http://sunflower.bio.indiana.edu/~gcg/genhelp/codonpreference.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}codonpreference $0 $1 $2 $4 $9 $10 $13 $7 $22 $6 $8 $12 $11 $14 $15 $16 $17 $5 $9999 $INfile1 coilscan local: Protein|Analysis|CoilScan TITLE CoilScan (GCG) INFO About Protein - Analysis - CoilScan (GCG) Main15 Main true 1 Threshold probability to predict a coiled-coil segment 0.5, 0.0, 1.0, 0.01 -PROBability 100 false 9 28 true -WINdow=28 10 21 false -WINdow=21 11 14 false -WINdow=14 12 Give increased weight to the first and fourth (hydrophobic)\npositions in the heptad repeat false -WEIght RSFFILE output biosequence/gcg coilscan.rsf output Save Coiled Coil features in -RSF Optional16 Optional false 2 Relative occurence of residues in the coiled-coil heptad repeat output biosequence/gcg mtidkcoils.dat output -DATa 4 output biosequence/gcg output File with position-by-position coiled-coil probabilities -TABle 5 Plot true 6 -PLOt 6 Include the threshold probability in the plot true -THReshold 7 Monitor the program progress in the Job Manager window false -MONitor 8 Display a summary at the end of the program in the Job Manager window false -SUMmary HELP Help for CoilScan http://sunflower.bio.indiana.edu/~gcg/genhelp/coilscan.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}coilscan $1 $100 $9 $100 $10 $100 $11 $100 $12 $RSFFILE $2 $4 $5 $6 $7 $8 $INfile $OUTfile1 compare local: Pairwise Comparison|Compare TITLE Compare (GCG) INFO About Pairwise Comparison - Compare (GCG) Main17 Main true 100 false 11 false word comparison 8,13 -MENu=WORdsize 8888 window/stringency comparison true 3,4,6,15,9999 Optional18 Optional false 6 output biosequence/gcg Prot ? blosum62.cmp : compardna.cmp output Scoring Matrix -MATRix 3 Comparison window Prot ? 30 : 21, 1, 50, 1 -WINdow 4 Set stringency for match in comparison window -STRIngency 8 Word size Prot ? 3 : 6, 1, 50, 1 -WORdsize 9 Maximum number of points to display 200000, 1, 200000, 1 -LIMit 15 false 12 true display single point under each matching window 9999 false display all points exceeding threshold under each matching window 10 -MENu=ALL 10 Point threshold Prot ? 2 : 1, 0, 200, 1 -ALL 13 true Sort points by diagonal 14,16 -SORtpoints 14 Set the minimum number of points on diagonal for sorting -MINPOints 16 false 17 display points on all diagonals true -MENu=RANdom 18 don't display points on diagonals with only a few points false HELP Help for Compare http://sunflower.bio.indiana.edu/~gcg/genhelp/compare.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 2 ${callgcg}compare $100 $11 $100 $100 $6 $3 $4 $8 $9 $15 $15 $9999 $15 $10 $13 $14 $16 $17 $16 $16 $INfile1 $INfile2 $OUTfile composition local: Nucleic|Gene Finding|Composition TITLE Composition (GCG) INFO About Nucleic - Gene Finding - Composition (GCG) globalrules !1 1 Optional19 Optional false 1 Determine composition of both strands of nucleic acids false -BOTHstrands 2 Include commas in the numbers in the output true -COMmas 3 Monitor program progress false -MONitor 4 Include screen summary at the end of the program false -SUMmary HELP Help for Composition http://sunflower.bio.indiana.edu/~gcg/genhelp/composition.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}composition $1 $2 $3 $4 $INfile $OUTfile consensus local: Nucleic|Gene Finding|Consensus TITLE Consensus (GCG) INFO About Nucleic - Gene Finding - Consensus (GCG) Main20 Main true 0 Input File Name input biosequence/gcg input -INfile 1 Percent certainty\nat which to find consensus 75.0, 0.0, 100.0, 1.0 -CERtainty HELP Help for Consensus http://sunflower.bio.indiana.edu/~gcg/genhelp/consensus.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}consensus $0 $1 $OUTfile corrupt local: Utilities|Sequence Utilities|Corrupt TITLE Corrupt (GCG) INFO About Utilities - Sequence Utilities - Corrupt (GCG) Main21 Main true 0 Number of substitutions\nto introduce 1, 0, 500, 1 -SUBstitutions 1 Number of length errors\nto introduce 1, 0, 500, 1 -INDels 7 output biosequence/gcg output List file of output sequence names -LIStfile Optional22 Optional false 2 Size of maximum insertion/deletion 3, 1, 250, 1 -MAXindel 3 Include the record of errors in the output file true -TRAce 4 corrupt Set output file name extension -EXTension 5 Show the screen monitor of input sequence names false -MONitor 6 Show the screen summary false -SUMmary HELP Help for Corrupt http://sunflower.bio.indiana.edu/~gcg/genhelp/corrupt.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}corrupt $0 $1 $7 $2 $3 $4 $5 $6 $INfile $OUTfile dataset local: Utilities|Database Utilities|DataSet TITLE DataSet (GCG) INFO About Utilities - Database Utilities - DataSet (GCG) globalrules Main23 Main true 100 false 21 Create a new data library true 20 Append the data to an existing data library false -MENu=APPend 22 Name of the data library -OUTfile1 Optional24 Optional false 0 The definition line identifier -IDToken 1 Prot ? P : N Type of sequences in this Dataset.\nP = Protein, N=Nucleic Acid -TYPe 2 The long logical name -LN 3 The short logical name -SN 4 Monitor program progress false -MONitor 5 Provide summary at the end of the program true -SUMmary 6 Create a VMS-specific record-oriented database true -VMSonly 7 Translate nucleotide sequence to protein false 8 -TOPROTein 8 output biosequence/gcg translate.txt output Translation table -TRANSlation HELP Help for DataSet http://sunflower.bio.indiana.edu/~gcg/genhelp/dataset.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}dataset $100 $100 $20 $100 $22 $0 $1 $2 $3 $4 $5 $6 $7 $8 $INfile distances local: Phylogeny|Distances TITLE Distances (GCG) INFO About Phylogeny - Distances (GCG) globalrules -4,-5,-16,!100,@2,@3 +4,+5,+16,100,@2,@3 Main25 Main true 100 false 1 false uncorrected distance 11,!12,13 -MENu1=1 2 true Jukes-Cantor distance 11,!12,13 -MENu1=2 3 true Kimura distance !11,!12,!13 -MENu1=3 4 false Jin-Nei gamma distance !11,12,!13 -MENu1=4 5 false Tajima-Nei distance !11,!12,!13 -MENu1=5 16 false Tamura distance !11,!12,!13 -MENu1=6 Optional26 Optional false 34082 false 6 false First position of each triplet -POSition=1 7 false Second position of each triplet -POSition=2 8 false Third position of each triplet -POSition=3 9 false First and second positions of each triplet -POSition=4 10 true All positions -POSition=5 13 Consider partial matches between degenerate symbols\n for uncorrected or Jukes-Cantor distance false -AMBIGuous 11 Gap weight\n for uncorrected or Jukes-Cantor distance 0.0, 0.0, 2.0, 0.1 -GAPweight 12 a' parameter\n for Jin-Nei gamma distance 1.0, 0.1, 2.0, 0.1 -APARAMeter 14 Create a report file\n containing the raw counts -FILe 15 Display a screen monitor of analysis progress false -MONitor HELP Help for Distances http://sunflower.bio.indiana.edu/~gcg/genhelp/distances.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}distances $100 $1 $100 $2 $100 $3 $100 $4 $100 $5 $100 $16 $100 $34082 $6 $34082 $7 $34082 $8 $34082 $9 $34082 $10 $34082 $13 $11 $12 $14 $15 $INfile $OUTfile diverge local: Phylogeny|Diverge TITLE Diverge (GCG) INFO About Phylogeny - Diverge (GCG) Main27 Main true 0 output biosequence/gcg translate.txt output Translation Scheme for Sequences -TRANSlate Optional28 Optional false 1 Output Ks and Ka matrices as individual files false -TOFiles HELP Help for Diverge http://sunflower.bio.indiana.edu/~gcg/genhelp/diverge.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}diverge $0 $1 $INfile1 $INfile2 $OUTfile domes local: Uncataloged|domes TITLE domes (GCG) INFO About Uncataloged - domes (GCG) Main29 Main true 20 Connect File input biosequence/gcg input -INfile Optional30 Optional false 100 false 7 ellipses true 5 rectangles false -MENu=RECtangles 6 diamond peaks false -MENu=PEAks 2 Display the sequence false -SHOwseq 4 Draw ticks true 3 -TICks 3 Number the ticks true 200 -NUMbering 200 Set the tick number interval -NUMbering 1 Ratio of the axes of the ellipse 0.8, 0.1, 2.0, .1 -MINortomajor 9998 Set the density false 9999 9999 Number of bases per 100 platen units -DENsity HELP Help for domes http://sunflower.bio.indiana.edu/~gcg/genhelp/domes.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}domes $20 $100 $100 $5 $100 $6 $100 $2 $4 $3 $200 $1 $9999 $INfile1 dotplot local: Pairwise Comparison|DotPlot Nucleic|Secondary Structure|Dotplot TITLE Dotplot (GCG) INFO About Nucleic - Secondary Structure - Dotplot (GCG) Main31 Main true 11 Point File input biosequence/gcg input -Infile1 Optional32 Optional false 9 Suppress connecting adjacent points with a line false -DOTSonly 7 Plot redundant points (when sequences are identical) false -ALL 10 Draw an axis of symmetry (when sequence is compared with its reverse) false -AXIs 1 Display the caption true -CAPtion 8 Connect ticks with a solid axis false -TICKAXes 2 Display labels true !444 -LABels 444 false 22 bottom false -TICKNUMbering=a 24 top true -TICKNUMbering=c 23 right true -TICKNUMbering=b 25 left false -TICKNUMbering=d 4 Color for the points 1, 1, 4, 1 -POIntcolor 100 false 28 point true 9,!6 -SYMbol=0 29 square false -SYMbol=1 30 octogon false -SYMbol=2 31 triangle false -SYMbol=3 32 + false -SYMbol=4 33 X false -SYMbol=5 34 diamond false -SYMbol=6 35 * false -SYMbol=7 36 | false -SYMbol=8 6 Change symbol height false 66 66 Height of centered symbols (in platen units) -SYMBOLHeight 9998 Set the density false 9999 9999 Number of bases per 100 platen units -DENsity HELP Help for Dotplot http://sunflower.bio.indiana.edu/~gcg/genhelp/dotplot.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}dotplot $11 $9 $7 $10 $1 $8 $2 $444 $22 $444 $24 $444 $23 $444 $25 $444 $4 $100 $28 $100 $29 $100 $30 $100 $31 $100 $32 $100 $33 $100 $34 $100 $35 $100 $36 $100 $66 $9999 $INfile1 fasta local: Database|Sequence Search|FastA TITLE FastA (GCG) INFO About Database - Sequence Search - FastA (GCG) Main33 Main true Optional34 Optional false 30 output biosequence/gcg Prot ? blosum50.cmp : fastadna.cmp output Scoring Matrix -MATRix 3 Set gap creation penalty -GAPweight 33 Set gap extension penalty -LENgthweight 6 Use PAM scoring matrix to calculate initial diagonal scores true -PAMfactor 5 Search only the top strand of nucleotide sequences false -ONEstrand 4 Search only sequences entered after a certain date false 44 44 Enter earliest date numerically as m.yy -SINce 1800 Only search sequences equal to or longer than false 18 18 Minimum length of search set sequence 500, 1, 1000, 100 -MINLength 1900 Only search sequences equal to or shorter than false 19 19 Maximum length of search set sequence 5000, 1000, 10000, 100 -MAXLength 16 Number of scores to list (regardless of E() value) 40, 1, 1000, 1 -LIStsize 15 Save and sort by optimized score true 150 -OPTall 150 Threshold for optimization (Program computes threshold if 0) 0, 0, 1000, 1 -OPTall 8 Suppress histogram in the output file false -NOHIStogram 9 Show sequence alignments in the output file true 7,10,11,17,20,21,22,23,24,99,100 -ALIGN 99 Number of alignments to show 0, 1, 1000, 1 -ALIGN 17 Use Smith-Waterman algorithm for final DNA-DNA alignment false -SWalign 7 Show complete sequences in alignment, not just overlaps false -SHOWall 11 Include sequence documentation in the alignment true -DOCLines 100 false 23 | = identities, : = conservative replacements true -MARKx=3 20 : = identities, . = conservative replacements false -MARKx=0 21 x = conservative replacements, X = non-conservative substitutions false -MARKx=1 22 show only residues in sequence 2 that differ from sequence 1 false -MARKx=2 24 write alignments in "parsable" format false -MARKx=10 10 Number of sequence symbols\n per line of the alignment 60, 60, 200, 60 -LINesize 130 Monitor sequences searched at intervals of 500 -MONitor HELP Help for FastA http://sunflower.bio.indiana.edu/~gcg/genhelp/fasta.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}fasta $30 $3 $33 $6 $5 $44 $18 $19 $16 $15 $150 $8 $9 $99 $17 $7 $11 $100 $23 $100 $20 $100 $21 $100 $22 $100 $24 $100 $10 $130 $INfile1 $INfile2 $OUTfile fastx local: Database|Sequence Search|FastX TITLE FastX (GCG) INFO About Database - Sequence Search - FastX (GCG) Main35 Main true Optional36 Optional false 30 output biosequence/gcg blosum50.cmp output Scoring Matrix -MATRix 3 Set gap creation penalty -GAPweight 33 Set gap extension penalty -LENgthweight 333 Set frame shift penalty -FRAmeweight 6 Use PAM scoring matrix to calculate initial diagonal scores true -PAMfactor 5 Search using only the top strand of the query sequence false -ONEstrand 4 Search only those sequences entered after a certain date false 44 44 Enter earliest date numerically as m.yy -SINce 1800 Only search sequences equal to or longer than false 18 18 Minimum length of search set sequence 500, 1, 1000, 100 -MINLength 1900 Only search sequences equal to or shorter than false 19 19 Maximum length of search set sequence 5000, 1000, 10000, 100 -MAXLength 16 Number of scores to list (regardless of E() value) 40, 1, 1000, 1 -LIStsize 15 Save and sort by optimized score true 150 -OPTall 150 Threshold for optimization (Program computes threshold if 0) 0, 0, 1000, 1 -OPTall 8 Suppress histogram in the output file false -NOHIStogram 9 Show sequence alignments in the output file true 7,10,11,17,20,21,22,23,24,99,100 -ALIGN 99 Number of alignments to show 0, 1, 1000, 1 -ALIGN 7 Show complete sequences in alignment, not just overlaps false -SHOWall 11 Include sequence documentation in the alignment true -DOCLines 100 false 23 | = identities, : = conservative replacements true -MARKx=3 20 : = identities, . = conservative replacements false -MARKx=0 21 x = conservative replacements, X = non-conservative substitutions false -MARKx=1 22 show only residues in sequence 2 that differ from sequence 1 false -MARKx=2 24 write alignments in "parsable" format false -MARKx=10 10 Number of sequence symbols\n per line of the alignment 60, 60, 200, 60 -LINesize 130 Monitor sequences searched at intervals of 500 -MONitor HELP Help for FastX http://sunflower.bio.indiana.edu/~gcg/genhelp/fastx.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}fastx $30 $3 $33 $333 $6 $5 $44 $18 $19 $16 $15 $150 $8 $9 $99 $7 $11 $100 $23 $100 $20 $100 $21 $100 $22 $100 $24 $100 $10 $130 $INfile1 $INfile2 $OUTfile findpatterns local: Database|Sequence Search|FindPatterns Nucleic|Gene Finding|FindPatterns TITLE FindPatterns (GCG) INFO About Nucleic - Gene Finding - FindPatterns (GCG) Main37 Main true Optional38 Optional false 100 false 5 search only the top strand of nucleotide sequences false -MENu=ONEstrand 99 search both strands of nucleotide sequences true 6 Show patterns composed of six or more symbols false -SIXbase 13 Show patterns that occur only once false !14,!15 -ONCe 14 Minimum number of occurrences 1, 0, 100000, 1 -MINCuts 15 Maximum number of occurrences 100000, 1, 100000, 1 -MAXCuts 16 Exclude patterns found between positions base1,base2 -EXCLude 8 Accept only perfect (nonambiguous) matches false -PERFect 3 Number of allowed mismatches in the pattern match 0, 0, 15, 1 -MISmatch 7 Do an "overlapping-set" search if nucleotide sequences false -ALL 4 Search only sequences entered after a certain date false 44 44 Enter earliest date numerically as m.yy -SINce 9 Append the pattern data file to the output file false -APPend 17 Format output as a list file of sequence names only false !11 -NAMes 10 Report every file searched even if there are no finds false !14 -SHOw 12 Display a screen trace showing each file searched false -MONitor HELP Help for FindPatterns http://sunflower.bio.indiana.edu/~gcg/genhelp/findpatterns.html IOFiles Input/Output files false INfile INfile INfilemsf input biosequence/msf input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} ${callgcg}findpatterns $100 $5 $100 $100 $6 $13 $14 $15 $16 $8 $3 $7 $44 $9 $17 $10 $12 $INfile $OUTfile fingerprint local: Mapping|Fingerprint TITLE Fingerprint (GCG) INFO About Mapping - Fingerprint (GCG) Optional39 Optional false 2 Don't sum statistics for identical fragments false -NOSUMidentical HELP Help for Fingerprint http://sunflower.bio.indiana.edu/~gcg/genhelp/fingerprint.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}fingerprint $2 $INfile1 $OUTfile1 fitconsensus local: Nucleic|Gene Finding|FitConsensus TITLE FitConsensus (GCG) INFO About Nucleic - Gene Finding - FitConsensus (GCG) Main40 Main true 9 Consensus table file input biosequence/gcg input -INfile2 0 100% positions must match exactly true -NECessary 1 Number of fits to show 40, 1, 999, 1 -LIStsize HELP Help for FitConsensus http://sunflower.bio.indiana.edu/~gcg/genhelp/fitconsensus.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}fitconsensus $9 $0 $1 $INfile1 $OUTfile foldrna local: Uncataloged|foldrna TITLE foldrna (GCG) INFO About Uncataloged - foldrna (GCG) Main41 Main true 1 false 100 normal run true 101 create file of folding matrix false 2,!30,!50,!60,!300,!301,!500,!501,!502 -MENu=SAVe 102 complete run using existing folding matrix file false !SQ1,3 -MENu=CONTinue 300 File with Text Representation of Folding output biosequence/gcg output -OUTfile1 301 Base-by-Base Output File -OUTfile2 2 output biosequence/gcg output Output File for Folding Matrix -SAVe 3 output biosequence/gcg output Input File with Folding Matrix -CONTinue Optional42 Optional false 302 Folding Energies output biosequence/gcg foldrna.energy output -DATa1 Exclude bases i through j from folding, ligating bases i-1 and j+1 together before folding. You may specify up to 9 of these regions. 50 i,j +51 -REMove1 51 i,j +52 -REMove2 52 i,j +53 -REMove3 53 i,j +54 -REMove4 54 i,j +55 -REMove5 55 i,j +56 -REMove6 56 i,j +57 -REMove7 57 i,j +58 -REMove8 58 i,j -REMove9 Force k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to force k consecutive bases, beginning with i, to form base pairs. You may specify up to 9 of these regions. 60 i,j,k +61 -FORCe1 61 i,j,k +62 -FORCe2 62 i,j,k +63 -FORCe3 63 i,j,k +64 -FORCe4 64 i,j,k +65 -FORCe5 65 i,j,k +66 -FORCe6 66 i,j,k +67 -FORCe7 67 i,j,k +68 -FORCe8 68 i,j,k -FORCe9 Prevent k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to prevent k consecutive bases, beginning with i, from base pairing. You may specify up to 9 of these regions. 30 i,j,k +31 -PREVent1 31 i,j,k +32 -PREVent2 32 i,j,k +33 -PREVent3 33 i,j,k +34 -PREVent4 34 i,j,k +35 -PREVent5 35 i,j,k +36 -PREVent6 36 i,j,k +37 -PREVent7 37 i,j,k +38 -PREVent8 38 i,j,k -PREVent9 HELP Help for foldrna http://sunflower.bio.indiana.edu/~gcg/genhelp/foldrna.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}foldrna $1 $1 $101 $1 $102 $1 $300 $301 $2 $3 $302 $50 $51 $52 $53 $54 $55 $56 $57 $58 $60 $61 $62 $63 $64 $65 $66 $67 $68 $30 $31 $32 $33 $34 $35 $36 $37 $38 $INfile framealign local: Pairwise Comparison|FrameAlign TITLE FrameAlign (GCG) INFO About Pairwise Comparison - FrameAlign (GCG) Optional43 Optional false 3 Scoring Matrix output biosequence/gcg blosum62.cmp output -MATRix 4 output biosequence/gcg output Translation Table -TRANSlate 0 Set gap creation penalty -GAPweight 1 Set gap extension penalty -LENgthweight 2 Set frameshift penalty -FRAmeweight 5 false 6 local alignment true 7 global alignment false 8,@23,@24 -MENu=GLObal 8 false 9 don't penalize gaps at the ends of the alignment true 10 penalize end gaps like other gaps false -MENu=ENDWeight 25 Don't penalize gap extensions longer than -PENAlizedlength 23 Gap shift limit for the nucleotide sequence 0, 0, 0, 1 -LIMit1 24 Gap shift limit for the protein sequence 0, 0, 0, 1 -LIMit2 11 false 12 minimum number of gaps true 13 maximum gaps in protein sequence (HighRoad) false -MENu=HIGhroad 14 maximum gaps in nucleotide sequence (LowRoad) false -MENu=LOWroad 26 Add gaps to restore the correct reading frame after frameshifts false -INFRame 15 Set thresholds for displaying '|', ':', and '.' (e.g. 4,2,1) -PAIr 16 Number of sequence symbols per line 50, 10, 150, 1 -WIDth 17 true Abbreviate large gaps in alignment with '.'s -BIGGaps 18 Number of lines of alignment per page 60, 4, 100, 1 -PAGe 19 New sequence file for nucleotide sequence with gaps added output biosequence/gcg nuc ? name(SQ1+.gap) : name(SQ2+.gap) output -OUTfile2 20 New sequence file for protein sequence with gaps added output biosequence/gcg nuc ? name(SQ2+.gap) : name(SQ1+.gap) output -OUTfile3 21 Monitor the program progress in the Job Manager window false -MONitor 22 Display a summary at the end of the program in the Job Manager window -SUMmary HELP Help for FrameAlign http://sunflower.bio.indiana.edu/~gcg/genhelp/framealign.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 2 ${callgcg}framealign $3 $4 $0 $1 $2 $5 $5 $7 $5 $8 $8 $10 $8 $25 $23 $24 $11 $11 $13 $11 $14 $11 $26 $15 $16 $17 $18 $19 $20 $21 $22 $INfile1 $INfile2 $OUTfile1 frames local: Nucleic|Gene Finding|Frames TITLE Frames (GCG) INFO About Nucleic - Gene Finding - Frames (GCG) Main44 Main true 0 output biosequence/gcg translate.txt output Translation Table -TRANSlate Optional45 Optional false 3 output biosequence/gcg ecohigh.cod output Codon Frequency Table -RARe 4 Threshold at or below which rare codons are shown 0.0, 0.0, 1.0, .1 -THReshold 2 Show all start and stop signals, not just open frames false -ALL 1 output biosequence/gcg output Mark File -Mark1 9998 Set the plot density false 9999 9999 Number of bases per 100 platen units -DENsity HELP Help for Frames http://sunflower.bio.indiana.edu/~gcg/genhelp/frames.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}frames $0 $3 $4 $2 $1 $9999 $INfile1 framesearch local: Database|Sequence Search|FrameSearch TITLE FrameSearch (GCG) INFO About Database - Sequence Search - FrameSearch (GCG) Main46 Main true Optional47 Optional false 27 Scoring Matrix output biosequence/gcg blosum62.cmp output -MATRix 28 output biosequence/gcg output Translation Table -TRANSlate 1 Set gap creation penalty -GAPweight 2 Set gap extension penalty -LENghtweight 3 Set frameshift penalty -FRAmeweight 4 Search only the top strand of nucleotide sequences false -ONEstrand 8 Scale scores as a function of sequence length false -SCAle 5 Number of scores to show @7 40, 1, 2500, 1 -LIStsize 6 true Display sequence alignments in the output file 7,15,20,21,22,23 -ALIgn 7 Number of alignments to show 0, 1, 0, 1 -ALIgn 9 false 10 local alignment true 11 global alignment false 12 -MENu=GLObal 12 false 13 don't penalize gaps at the ends of the alignment true 14 penalize end gaps like other gaps false -MENu=ENDWeight 29 Don't penalize gap extensions longer than -PENAlizedlength 15 false 16 minimum number of gaps true 17 maximum gaps in protein sequence (HighRoad) false -MENu=HIGhroad 18 maximum gaps in nucleotide sequence (LowRoad) false -MENu=LOWroad 40 Add gaps to restore the correct reading frame after frameshifts false -INFRame 19 Length of documentation for each sequence in the output list 70, 40, 150, 1 -LINesize 20 Number of sequence symbols per line in alignments 50, 10, 150, 1 -WIDth 21 Set thresholds for displaying '|', ':', and '.' in alignments (e.g. 4,2,1) -PAIr 22 true Abbreviate large gaps in alignments with '.'s -BIGGaps 23 Number of lines of alignment per page 60, 4, 100, 1 -PAGe 24 Plot the distribution of alignment scores true -PLOt 25 Monitor sequences searched at intervals of 100 -MONitor 26 Provide summary at the end of the program false -SUMmary 1000 Compare forward and reverse alignment scores for\n each sequence searched false -VALIDATE HELP Help for FrameSearch http://sunflower.bio.indiana.edu/~gcg/genhelp/framesearch.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}framesearch $27 $28 $1 $2 $3 $4 $8 $5 $6 $7 $9 $9 $11 $9 $12 $12 $14 $12 $29 $15 $15 $17 $15 $18 $15 $40 $19 $20 $21 $22 $23 $24 $25 $26 $1000 $INfile1 $INfile2 $OUTfile fromembl local: Import/Export|FromEMBL TITLE FromEMBL (GCG) INFO About Import/Export - FromEMBL (GCG) Main48 Main true 8 EMBL sequence data file input biosequence/gcg input -INfile 3 output biosequence/gcg output List file of output sequence names -LIStfile Optional49 Optional false 100 false 20 nucleic acid false -MENu=NUCleotide 21 protein false -MENu=PROtein 2 Write output to a different directory -DIRectory 0 Show the screen monitor of input sequence names false -MONitor 1 Include screen summary at the end of the program false -SUMmary HELP Help for FromEMBL http://sunflower.bio.indiana.edu/~gcg/genhelp/fromembl.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}fromembl $8 $3 $100 $20 $100 $21 $100 $2 $0 $1 fromfasta local: Import/Export|FromFastA TITLE FromFastA (GCG) INFO About Import/Export - FromFastA (GCG) Main50 Main true 0 FastA sequence file input biosequence/gcg input -INfile 3 output biosequence/gcg output List file of output sequence names -LIStfile Optional51 Optional false 100 false 20 nucleic acid false -MENu=NUCleotide 21 protein false -MENu=PROtein HELP Help for FromFastA http://sunflower.bio.indiana.edu/~gcg/genhelp/fromfasta.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}fromfasta $0 $3 $100 $20 $100 $21 $100 fromgenbank local: Import/Export|FromGenBank TITLE FromGenBank (GCG) INFO About Import/Export - FromGenBank (GCG) Main52 Main true 0 GenBank sequence data file input biosequence/gcg input -INfile 3 output biosequence/gcg output List file of output sequence names -LIStfile Optional53 Optional false 100 false 20 nucleic acid false -MENu=NUCleotide 21 protein false -MENu=PROtein 2 Write output to a different directory -DIRectory 1 Show the screen monitor of output sequence names false -MONitor 4 Include screen summary at the end of the program false -SUMmary HELP Help for FromGenBank http://sunflower.bio.indiana.edu/~gcg/genhelp/fromgenbank.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}fromgenbank $0 $3 $100 $20 $100 $21 $100 $2 $1 $4 fromig local: Import/Export|FromIG TITLE FromIG (GCG) INFO About Import/Export - FromIG (GCG) Main54 Main true 0 IntelliGenetics sequence file input biosequence/gcg input -INfile 3 output biosequence/gcg output List file of output sequence names -LIStfile Optional55 Optional false 100 false 20 nucleic acid false -MENu=NUCleotide 21 protein false -MENu=PROtein HELP Help for FromIG http://sunflower.bio.indiana.edu/~gcg/genhelp/fromig.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}fromig $0 $3 $100 $20 $100 $21 $100 frompir local: Import/Export|FromPIR TITLE FromPIR (GCG) INFO About Import/Export - FromPIR (GCG) Main56 Main true 0 PIR sequence data file input biosequence/gcg input -INfile 3 output biosequence/gcg output List file of output sequence names -LIStfile Optional57 Optional false 100 false 20 nucleic acid false -MENu=NUCleotide 21 protein false -MENu=PROtein 2 Write output to a different directory -DIRectory 1 gcg File name extension for output sequence files -EXTension 4 Show the screen monitor of output sequence names false -MONitor 5 Include screen summary at the end of the program false -SUMmary HELP Help for FromPIR http://sunflower.bio.indiana.edu/~gcg/genhelp/frompir.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}frompir $0 $3 $100 $20 $100 $21 $100 $2 $1 $4 $5 fromstaden local: Import/Export|FromStaden TITLE FromStaden (GCG) INFO About Import/Export - FromStaden (GCG) Main58 Main true 0 Staden sequence file input biosequence/gcg input -INfile Optional59 Optional false 100 false 2 nucleic acid false -MENu=NUCleotide 3 protein false -MENu=PROtein 4 Show the screen monitor of program progress false -MONitor HELP Help for FromStaden http://sunflower.bio.indiana.edu/~gcg/genhelp/fromstaden.html IOFiles Input/Output files false INfile1 INfile1 INfile1msf input biosequence/msf input -INfile1=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}fromstaden $0 $100 $2 $100 $3 $100 $4 $INfile1 $OUTfile1 gap local: Pairwise Comparison|Gap TITLE Gap (GCG) INFO About Pairwise Comparison - Gap (GCG) Optional60 Optional false 20 output biosequence/gcg prot ? blosum62.cmp : nwsgapdna.cmp output Scoring Matrix -MATRix 3 Set gap creation penalty -GAPweight 4 Set gap extension penalty -LENgthweight 100 false 160 don't penalize gaps at the ends of the alignment true 16 penalize end gaps like other gaps false -MENu=ENDWeight 31 Don't penalize gap extensions longer than -PENAlizedlength 8 Gap shift limit for sequence 1 0, 0, 0, 1 -LIMit1 22 Gap shift limit for sequence 2 0, 0, 0, 1 -LIMit2 32028 false 10 select "top" alignment for equally optimal alignment (HighRoad) false -MENu=HIGhroad 11 select "bottom" alignment for equally optimal alignment (LowRoad) false -MENu=LOWroad 82600 false Generate statistics from randomized alignments 9,101 -RANdomizations 101 false 102 nucleotide or amino acid composition true 103 dinucleotide or dipeptide composition false -PREServe=2 104 trinucleotide or tripeptide composition false -PREServe=3 9 Number of randomizations 10, 2, 100, 1 -RANdomizations 13 Set thresholds for displaying '|', ':', and '.' (e.g. 4,2,1) -PAIr 12 Number of sequence symbols per line 50, 10, 150, 1 -WIDth 14 Number of lines per page 60, 4, 100, 1 -PAGe 15 true Abbreviate large gaps with '.'s -BIGGaps 6 output biosequence/gcg name(SQ1+.gap) output New sequence file for sequence 1 with gaps added -OUTfile2 7 output biosequence/gcg name(SQ2+.gap) output New sequence file for sequence 2 with gaps added -OUTfile3 18 Include the summary at the end of the program false -SUMmary HELP Help for Gap http://sunflower.bio.indiana.edu/~gcg/genhelp/gap.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 2 ${callgcg}gap $20 $3 $4 $100 $100 $16 $100 $31 $8 $22 $32028 $10 $32028 $11 $32028 $82600 $101 $101 $103 $101 $104 $101 $9 $13 $12 $14 $15 $6 $7 $18 $INfile1 $INfile2 $OUTfile1 gapshow local: Pairwise Comparison|GapShow TITLE GapShow (GCG) INFO About Pairwise Comparison - GapShow (GCG) Optional61 Optional false 2 output biosequence/gcg prot ? blosum62.cmp : swgapdna.cmp output Scoring Matrix -MATRix 7 Plot true 999,21,9,56,9998,4,5 -PLOt 999 false 8 false plot bars for similarities -MENu=s 20 true plot bars for differences -MENu=d 9 Represent the sequences as continuous (unbroken) lines false -CONtinuous 21 Include titles above and below the plot true -LABeling 56 Number the sequences true 60,61,62,63 -NUMbering 60 Number sequence 1 downwards (default is upwards) false @61 -REVNUM1 61 #60 ? eval(SQ1.end) : eval(SQ1.begin) Start numbering sequence 1 at -NUM1 62 Number sequence 2 downwards (default is upwards) false @63 -REVNUM2 63 #62 ? eval(SQ2.end) : eval(SQ2.begin) Start numbering sequence 2 at -NUM2 4 output biosequence/gcg output Mark File for Sequence 1 -MARk1 5 output biosequence/gcg output Mark File for Sequence 2 -MARk2 9998 Set the density false 9999 9999 Number of bases per 100 platen units -DENsity 6 output biosequence/gcg name(SQ1+.pair) output Create a paired output file like the one from GAP 13,14,12,15 -OUTfile1 13 Set thresholds for displaying '|', ':', and '.' (e.g. 4,2,1) -PAIr 14 Number of lines per page 60, 4, 100, 1 -PAGe 12 Number of sequence symbols per line 50, 10, 150, 1 -WIDth 15 true Abbreviate large gaps with '.'s -BIGGaps HELP Help for GapShow http://sunflower.bio.indiana.edu/~gcg/genhelp/gapshow.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 2 ${callgcg}gapshow $2 $7 $999 $8 $999 $20 $999 $9 $21 $56 $60 $61 $62 $63 $4 $5 $9999 $6 $13 $14 $12 $15 $INfile1 $INfile2 gcgtoblast local: Utilities|Database Utilities|GCGToBlast TITLE GCGToBlast (GCG) INFO About Utilities - Database Utilities - GCGToBlast (GCG) Main62 Main true 100 Name of the output files -OUTfile1 Optional63 Optional false 0 Write into the directory specified below\nrather than into the current directory false 1 1 Directory specification -DIRectory 5 Make streamlf files instead or record-oriented files false -NOVMSonly 7 Create multi-volume database false 8 8 Number of sequence characters per volume (0-2,000,000,000) 0 -VOLsize 2 Delete the FASTA-format data after the database generation true -DELete 3 Monitor progress with a screen trace false -MONitor 4 Include the summary at the end of the program false -SUMmary HELP Help for GCGToBlast http://sunflower.bio.indiana.edu/~gcg/genhelp/gcgtoblast.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}gcgtoblast $100 $1 $5 $8 $2 $3 $4 $INfile gelassemble local: Fragment Assembly|GelAssemble ${callgcg}seqlabgelassemble TITLE GelAssemble (GCG) INFO About Fragment Assembly - GelAssemble (GCG) Optional64 Optional false 0 ContigName Load the specified contig directly into the Edit Screen. -CONTIG 1 lets you scroll through the GELOVERLAP clusters -CLUSTER 2 Number of screen rows 24, 16, 100, 1 -WPIROWS 3 Number of screen columns 80, 80, 300, 1 -WPICOLS HELP Help for GelAssemble http://sunflower.bio.indiana.edu/~gcg/genhelp/gelassemble.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 geldisassemble local: Uncataloged|geldisassemble TITLE geldisassemble (GCG) INFO About Uncataloged - geldisassemble (GCG) Optional65 Optional false 0 false 1 original gel readings false -MENu=ARChive 2 edited fragments true 3 Show the screen monitor of program progress false -MONitor HELP Help for geldisassemble http://sunflower.bio.indiana.edu/~gcg/genhelp/geldisassemble.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}geldisassemble $0 $1 $0 $0 $3 gelenter local: Fragment Assembly|GelEnter ${callgcg}seqlabgelenter TITLE GelEnter (GCG) INFO About Fragment Assembly - GelEnter (GCG) globalrules Main66 Main true 100 false 20 Enter the selected sequences from the Main Window true -WPIMENU=1 21 Enter a new sequence false !SQ1 -WPIMENU=2 22 Enter existing sequence files as specified below false 23,24,!SQ1 -WPIMENU=3 23 Sequence files to enter -ENTER 24 Files are in Staden format false -STAden Optional67 Optional false 0 Automatically return to screen mode after commands false -SINGlecommand 1 Set find to search for perfect symbol matches false -PERFect 2 Highlight these sequences -VECtors 3 Highlight these patterns -SITes 4 G,A,T,C The default lane order for the digitizer -LANes 5 Minimum overlap length for Reload command 10, 1, 50, 1 -MINOverlap 6 Stringency for the Reload command 95, 50, 100, 1 -PCTOverlap 7 tolerance for digitizing ambiguity (0 to 1)1 being the most tolerant 0.4, , , -TOLerance HELP Help for GelEnter http://sunflower.bio.indiana.edu/~gcg/genhelp/gelenter.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 gelmerge local: Fragment Assembly|GelMerge TITLE GelMerge (GCG) INFO About Fragment Assembly - GelMerge (GCG) Main68 Main true 0 Word size for overlap determination @2,@5,@14 7, 1, 30, 1 -WORdsize 1 Minimum fraction of matching words in overlap 0.8, 0.0, 1.0, 0.01 -STRIngency 2 Minimum overlap length @5,@14 0, 0, 1000, 1 -MINOverlap Optional69 Optional false Contig Assembly: 100 false 9 original gel readings false -MENu=ARChive 10 individual edited fragments (with gaps removed) false -MENu=WORKing 18 current contigs true 1002 Suppress contig assembly false !5,!6,!3,!7,!8 -MENu=WPISUPPRESSMERGE 5 Minimum run of identical bases found at least\nonce in an overlap between two contigs 0, 0, 0, 1 -MINIdentity 6 Maximum gap size in overlap determination 10, 0, 100, 1 -MAXGap 3 output biosequence/gcg gelmergedna.cmp output Scoring matrix for contig assembly -MATRix1 7 Gap creation penalty in contig assembly 8, 0, 100, 1 -GAPweight 8 Gap extension penalty in contig assembly 2, 0, 100, 1 -LENgthweight Vector Recognition and Excision: 12 Remove vector sequences from single-fragment contigs false 13,14,15,4,16,17 -EXCise 11 output biosequence/gcg output Output file of alignments between fragment and vector sequences 13,14,15,4,16,17 -REPortfile 13 Minimum fraction of matches in vector recognition 0.8, 0.5, 1.0, .1 -VECTORSTrigency 14 Minimum run of identical bases found at least\nonce in a match between vector and fragment 0, 0, 4000, 1 -VECTORMINIdentity 15 Maximum gap size in first step of vector recognition 5, 0, 100, 1 -VECTORMAXGap 4 output biosequence/gcg gelmergelocaldna.cmp output Scoring matrix for vector recognition -MATRix2 16 Gap creation penalty in vector recognition 30, 0, 200, 1 -VECTORGAPweight 17 Gap extension penalty in vector recognition 3, 0, 200, 1 -VECTORLENgthweight 19 Monitor vector recognition and contig assembly false -MONitor 20 Include screen summary at the end of the program false -SUMmary 21 submits program to the batch queue false -BATch HELP Help for GelMerge http://sunflower.bio.indiana.edu/~gcg/genhelp/gelmerge.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}gelmerge $0 $1 $2 $100 $9 $100 $10 $100 $100 $1002 $100 $5 $6 $3 $7 $8 $12 $11 $13 $14 $15 $4 $16 $17 $19 $20 $21 gelstart local: Fragment Assembly|GelStart TITLE GelStart (GCG) INFO About Fragment Assembly - GelStart (GCG) Main70 Main true 3 Project Name -NAME 100 false 4 Begin a new project false -MENu=NEWproject 5 Identify an existing project true 44 Delete an existing project false -MENu=DELete Optional71 Optional false 0 Recognize these vector sequences in GELENTER and GELMERGE -VECtors 1 Highlight these sequence patterns in GELENTER -SITes 7 Show the screen monitor of program progress false -MONitor HELP Help for GelStart http://sunflower.bio.indiana.edu/~gcg/genhelp/gelstart.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}gelstart $3 $100 $4 $100 $100 $44 $100 $0 $1 $7 gelview local: Fragment Assembly|GelView TITLE GelView (GCG) INFO About Fragment Assembly - GelView (GCG) Optional72 Optional false 1 Include the fragment bar diagrams true -BAR HELP Help for GelView http://sunflower.bio.indiana.edu/~gcg/genhelp/gelview.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}gelview $1 $OUTfile growtree local: Phylogeny|GrowTree TITLE GrowTree (GCG) INFO About Phylogeny - GrowTree (GCG) Main73 Main true 15 Distance Matrix from Distances input biosequence/gcg input -INfile 100 false 1 true Neighbor joining -MENu=1 2 false UPGMA -MENu=2 Optional74 Optional false 5 Don't report branch lengths in trees file false !3,!4 -NOBRanch 3 Report negative branch lengths as zero false -NONEGative 4 Report branch lengths to nearest integer false -ROUND 94031 false 6 true keep original order of sequence names -ORDer=0 7 false sort alphabetically by ascending name -ORDer=1 8 false sort alphabetically by descending name -ORDer=2 9 false ladder to left -ORDer=3 10 false ladder to right -ORDer=4 14 Suppress graphical display of tree false !11,!12,!13 -NOPLOt 13 false 11 true phylogram -TREEFORMat=1 12 false cladogram -TREEFORMat=2 HELP Help for GrowTree http://sunflower.bio.indiana.edu/~gcg/genhelp/growtree.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}growtree $15 $100 $1 $100 $2 $100 $5 $3 $4 $94031 $6 $94031 $7 $94031 $8 $94031 $9 $94031 $10 $94031 $14 $13 $11 $13 $12 $13 $OUTfile helicalwheel local: Protein|Analysis|HelicalWheel TITLE HelicalWheel (GCG) INFO About Protein - Analysis - HelicalWheel (GCG) Optional75 Optional false 1 output biosequence/gcg simplify.txt output Simplify sequence using symbol equivalences in file -SIMplify 0 output biosequence/gcg helicalwheel.dat output File of charge and color attributes for each amino acid -DATa 2 Angle of rotation per residue 100.0, 0.0, 360.0, .1 -ANGle 3 Angle of rotation set for beta structures (160 degrees) false !2 -BETa 7 Draw box around hydrophobic residues true -CHArge 6 false 60 single letter amino acid code true 61 three letter amino acid codes false -MENu=THRee 4 Radius of wheel in platen units 30.0, 0.0, 75.0, .1 -RADius 5 Angular position of first residue on wheel (0.0 is 12 o'clock) 0.0, 0.0, 360.0, .1 -STArtposition HELP Help for HelicalWheel http://sunflower.bio.indiana.edu/~gcg/genhelp/helicalwheel.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}helicalwheel $1 $0 $2 $3 $7 $6 $6 $61 $6 $4 $5 $INfile hmmeralign local: Multiple Comparison|HmmerAlign HMMER|HmmerAlign TITLE HmmerAlign (GCG) INFO About HMMER - HmmerAlign (GCG) Main76 Main true 1 profile HMM to use input biosequence/gcg input -INfile1 Optional77 Optional false 5 false Include in the alignment only those residues that\nalign to match states in the model -MATch Combine output alignment and ... 6 original HMM alignment false 60 HELP Help for HmmerAlign http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmeralign.html IOFiles Input/Output files false INfile2 INfile2 INfile2msf input biosequence/msf input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmeralign $1 $5 $INfile2 $OUTfile hmmerbuild local: HMMER|HmmerBuild TITLE HmmerBuild (GCG) INFO About HMMER - HmmerBuild (GCG) Main78 Main true 100 false 3 create a new HMM true -2 4 append the HMM to an existing HMM database false -6 -MENu=APPend 5 overwrite an existing HMM false -6 -MENu=OVERwrite 2 output biosequence/gcg output Name of HMM Output File Prot ? -23 : -24 -OUTfile 20 Internal name for profile HMM -NAME 10 false 11 true multiple global !21,!22 -MENu=G 12 false multiple local 21,22 -MENu=L 13 false single global !21,!22 -MENu=B 14 false single local 21,22 -MENu=C Optional79 Optional false 21 Probability that local alignment begins at left end of model 0.5, 0, 1, 0.01 -SWEntry 22 Probability that local alignment ends at right end of model 0.5, 0, 1, 0.01 -SWExit 23 false Force sequence alignment to be interpreted\nas amino acid sequences -PROtein 24 false Force sequence alignment to be interpreted\nas nucleic acid sequences -DNA 25 Architecture prior used by MAP construction algorithm 0.85, 0, 1, 0.01 -ARCHprior 40 false Fast heuristic determination of model architecture 41 -FASt 41 Assign columns to insert states if gap character fraction is 0.5, 0, 1, 0.01 -GAPS 26 output biosequence/gcg output Use this null model instead of the default null model -NULlmodel 45543 false 27 use default Dirichlet prior true 50 use a substitution matrix-based prior false +61,+62 60 use your own Dirichlet prior false +51 51 Dirichlet prior filename output biosequence/gcg output -DIRIchlet 61 Substitution matrix to use as prior output biosequence/gcg output -MATRix 62 Number of pseudocounts contributed by substitution matrix prior 20.0, 0, 1000, 0.01 -MATWeight 29 false Use true number of sequences instead of\neffective sequence number -NOEffseqnum 30 false 300 true use Gerstein/Sonnhammer/Chothia sequence weighting 301 false use BLOSUM sequence weighting -WEIghting=B 302 false use Krogh/Mitchison maximum entropy sequence weighting -WEIghting=M 303 false use Sibbald/Argos Voronoi sequence weighting -WEIghting=V 304 false turn off built-in sequence weighting -WEIghting=N 31 Determination of effective sequence number and clustering threshold for BLOSUM sequence weighting 0.62, 0, 1, 0.01 -CLUSTERLevel 32 false Print extra information -VERbose HELP Help for HmmerBuild http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmerbuild.html IOFiles Input/Output files false INfile1 INfile1 ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}hmmerbuild $100 $100 $4 $100 $5 $100 $2 $20 $10 $11 $10 $12 $10 $13 $10 $14 $10 $21 $22 $23 $24 $25 $40 $41 $26 $45543 $45543 $45543 $45543 $51 $61 $62 $29 $30 $30 $301 $30 $302 $30 $303 $30 $304 $30 $31 $32 $INfile1 hmmercalibrate local: HMMER|HmmerCalibrate TITLE HmmerCalibrate (GCG) INFO About HMMER - HmmerCalibrate (GCG) Main80 Main true 1 Profile HMM to calibrate input biosequence/gcg input -INfile 2 Number of processors to use 1, 1, 4, 1 -PROCessors Optional81 Optional false 11 Number of random sequences to generate 5000, 1, 100000, 1 -SEQNUM 12 false Fix the length of the random sequences at ... 120,!13,!14 120 Specify fixed length value , 1, 1000, 1 -LENgth 13 Set the mean length of random sequences to 350, 1, 1000, 1 -MEAnlength 14 Set the standard deviation of the random sequence length distribution to 350, 1, 1000, 1 -STDdevlength 15 Set the random number generator seed to , 1, 1000000, 1 -SEED 16 Save histogram of scores to this file output biosequence/gcg output -HIStogram HELP Help for HmmerCalibrate http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmercalibrate.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmercalibrate $1 $2 $11 $120 $13 $14 $15 $16 hmmerconvert local: HMMER|HmmerConvert TITLE HmmerConvert (GCG) INFO About HMMER - HmmerConvert (GCG) Main82 Main true 1 HMM input biosequence/gcg input -INfile 10 false 11 true ASCII -MENu=a 12 false binary -MENu=b 13 false GCG profile -MENu=p 14 false append to output file -MENu=e 15 false overwrite the output file -MENu=o 100 Name of output file -OUTfile HELP Help for HmmerConvert http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmerconvert.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmerconvert $1 $10 $11 $10 $12 $10 $13 $10 $14 $10 $15 $10 $100 hmmeremit local: HMMER|HmmerEmit TITLE HmmerEmit (GCG) INFO About HMMER - HmmerEmit (GCG) Main83 Main true 1 Profile HMM to use input biosequence/gcg input -INfile Optional84 Optional false 100 false 10 true write sequences in RSF unaligned format 11 false write sequences in RSF aligned format -MENu=MULTIAlign 12 false create a single majority-rule consensus sequence -13 -MENu=CONsensus 13 Number of sequences to generate 10, 1, 1000, 1 -SEQNUM 14 Set the random number generator seed to , 1, 1000000, 1 -SEED HELP Help for HmmerEmit http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmeremit.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmeremit $1 $100 $100 $11 $100 $12 $100 $13 $14 $OUTfile hmmerfetch local: HMMER|HmmerFetch TITLE HmmerFetch (GCG) INFO About HMMER - HmmerFetch (GCG) Main85 Main true 1 HMM name -INfile1 2 HMM Database input biosequence/gcg input Prot ? 20 : -20 -INfile2 HELP Help for HmmerFetch http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmerfetch.html IOFiles Input/Output files false OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmerfetch $1 $2 $OUTfile hmmerindex local: HMMER|HmmerIndex TITLE HmmerIndex (GCG) INFO About HMMER - HmmerIndex (GCG) Main86 Main true 1 HMM Database input biosequence/gcg input -INfile1 HELP Help for HmmerIndex http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmerindex.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmerindex $1 hmmerpfam local: HMMER|HmmerPfam Protein|Analysis|HmmerPfam TITLE HmmerPfam (GCG) INFO About Protein - Analysis - HmmerPfam (GCG) Main87 Main true 2 Profile HMM database input biosequence/gcg input Prot ? 20 : -20 -INfile2 3 output biosequence/gcg hmmerpfam.rsf output Save the best scoring profile HMMs as features in an RSF file -RSF 4 Number of processors to use 1, 1, 4, 1 -PROCessors Optional88 Optional false 11 false Insist that models and sequences are nucleic acid !20 -DNA 20 false Filter protein sequences with XNU to remove tandem repeats -XNU 12 Limit number of aligments of best scoring domains false 120 120 Specify limit , 1, 1000, 1 -LIMit 13 Set E-value cutoff for the sequence list 10.0, 0.0, 100.0, 0.01 -EVCutoff 15 false Set E-value cutoff for the domain list 150 150 Specify cutoff value , 0.0, 100.0, 0.1 -DOMEVcutoff 14 false Set bit score cutoff for the sequence list 140 140 Specify cutoff value , -1000.0, 1000.0, 1.0 -BSCUtoff 16 false Set bit score cutoff for the domain list 160 160 Specify cutoff value , -1000.0, 1000.0, 1.0 -DOMBScutoff 17 Calculate the E-values as if the database contained\nthis number of sequences 59021, 1, 100000, 1 -EVSeqnum 18 false Use Forward algorithm to determine sequence scores -FORWard 19 false Turn off the post hoc second null model -NULL2 HELP Help for HmmerPfam http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmerpfam.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}hmmerpfam $2 $3 $4 $11 $20 $120 $13 $150 $140 $160 $17 $18 $19 $INfile1 $OUTfile hmmersearch local: Database|Sequence Search|HmmerSearch HMMER|HmmerSearch TITLE HmmerSearch (GCG) INFO About HMMER - HmmerSearch (GCG) Main89 Main true 1 Profile HMM to use as query input biosequence/gcg input -INfile1 Optional90 Optional false 5 Maximum number of alignments of best scoring domains to display 100000, 1, 60000, 1 -LIMit 6 Set E-value cutoff for the list of best sequences 10.0, 0.0, 100.0, 0.01 -EVCutoff 9 false Set E-value cutoff for the list of best domains 90 90 Specify cutoff value , 0.0, 100.0, 0.01 -DOMEVcutoff 7 false Set bit score cutoff for the best sequences list 70 70 Specify cutoff value , -1000.0, 1000.0, 1.0 -BSCUtoff 10 false Set bit score cutoff for the best domains list 100 100 Specify cutoff value , -1000.0, 1000.0, 1.0 -DOMBScutoff 8 Calculate E-values as if the database contained\nthis number of sequences 59021, 1, 100000, 1 -EVSeqnum 11 false Use Forward algorithm to determine sequence scores -FORWard 12 false Turn off the post hoc second null model -NULL2 13 false Filter protein sequences with XNU to remove tandem repeats -XNU 14 false Display whole sequences instead of domains in the second list -NOFRAgments HELP Help for HmmerSearch http://sunflower.bio.indiana.edu/~gcg/genhelp/hmmersearch.html IOFiles Input/Output files false INfile2 INfile2 INfile2msf input biosequence/msf input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}hmmersearch $1 $5 $6 $90 $70 $100 $8 $11 $12 $13 $14 $INfile2 $OUTfile hthscan local: Protein|Analysis|HTHScan TITLE HTHScan (GCG) INFO About Protein - Analysis - HTHScan (GCG) Main91 Main true HTHFAMILY false ARAC araC true /FAMily=ARAC LYSR lysR false /FAMily=LYSR HOMEOBOX Homeobox false /FAMily=HOMEOBOX THRESHOLD Minimum acceptable score for H-T-H motifs 4.0, -20.0, 80.0, 0.1 -THRESHold RSFFILE output biosequence/gcg hthscan.rsf output Save Helix-Turn-Helix features in -RSF Optional92 Optional false NUMTOPSCORES Maximum number of H-T-H motifs to report 100, 1, 100, 1 -NUMTOPscores LOCALDATA Local weight matrix file !HTHFAMILY -DATa PROBABILITIES Compute probabilities for scores true EVEN -PROBabilities EVEN Assume even residue distribution in input sequence false -EVEn VERBOSE Verbose output false -VERbose MONITOR Show progress after how many files or sequences? 10, 1, 1000, 1 -MONitor SUMMARY Print summary information to screen at exit false -SUMmary FAITHFUL Always display full sequence documentation in reports false -FAITHful HELP Help for HTHScan http://sunflower.bio.indiana.edu/~gcg/genhelp/hthscan.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}hthscan $HTHFAMILY $ARAC $HTHFAMILY $LYSR $HTHFAMILY $HOMEOBOX $HTHFAMILY $THRESHOLD $RSFFILE $NUMTOPSCORES $LOCALDATA $PROBABILITIES $EVEN $VERBOSE $MONITOR $SUMMARY $FAITHFUL $INfile $OUTfile isoelectric local: Protein|Analysis|Isoelectric TITLE Isoelectric (GCG) INFO About Protein - Analysis - Isoelectric (GCG) Optional93 Optional false 0 output biosequence/gcg isoelectric.dat output Amino Acid pK Data File -DATa 1 output biosequence/gcg name(SQ1+.iso) output File containing the number of hydrogen ions bound\nand net charge at each pH point. -OUTfile 2 Number of protein amino terminii 1, 0, 100, 1 -AMINotermini 3 Number of protein carboxyl terminii 1, 0, 100, 1 -CARBoxyltermini 4 pH increment for charge calculation 0.5, 0.01, 12.0, 0.01 -PHDelta 5 Plot true 6,7 -PLOt 6 Minimum net charge to plot @7 50, -500, 500, 0 -MINCharge 7 Maxmimum net charge to plot 0, 0, 0, 0 -MAXCharge HELP Help for Isoelectric http://sunflower.bio.indiana.edu/~gcg/genhelp/isoelectric.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}isoelectric $0 $1 $2 $3 $4 $5 $6 $7 $INfile lookup local: Database|Text Search|LookUp TITLE LookUp (GCG) INFO About Database - Text Search - LookUp (GCG) Main94 Main true 100 false 40 false Search the sequences chosen in the Main Window !42 41 true Search the chosen sequence libraries !SQ1 42 false 32 GenBank false -LIBrary=GENBANK 35 GenBank EST false -LIBrary=GB_EST 15 GenBank GSS false -LIBrary=GB_GSS 31 EMBL false -LIBrary=EMBL 34 EMBL EST false -LIBrary=EM_EST 43 EMBL GSS false -LIBrary=EM_GSS 30 SwissProt true -LIBrary=SWISSPROT 36 SPTREMBL false -LIBrary=SPTREMBL 33 PIR false -LIBrary=PIR 39 NRL_3D false -LIBrary=NRL_3D 14 All text -ALLtext 9 Definition -DEFInition 3 Author -AUThor 5 Keyword -KEYword 1 Seq. name -NAMe 2 Accession -ACCessionnumber 4 Organism -ORGanism 7 Reference -REFerence 6 Pub. title -TITle 8 Feature -FEAture Optional95 Optional false 10 Longest sequence length -LONgest 11 Shortest sequence length -SHOrtest 12 Sequences dated on or before dd-mon-yyyy -LATest 13 Sequences dated on or after dd-mon-yyyy -EARliest 16 Turn off automatic wildcard extension false -NOWILdcardextension 399 Annotate sequences in the output file true 400 -ANNotate 400 false 410 Definition true -ANNotate=DEFinition 401 Accession number false -ANNotate=ACCession 402 Author false -ANNotate=AUThor 403 Date false -ANNotate=DATe 404 Features false -ANNotate=FEAtures 405 ID false -ANNotate=ID 406 Keywords false -ANNotate=KEYwords 407 Organism false -ANNotate=ORGanism 408 Reference false -ANNotate=REFerence 409 Title false -ANNotate=TITle 24 Show features as fragments instead of as whole entries false -FRAgments 25 Show only features with unambiguous coordinates false -COMplete HELP Help for LookUp http://sunflower.bio.indiana.edu/~gcg/genhelp/lookup.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}lookup $100 $100 $100 $42 $32 $42 $35 $42 $15 $42 $31 $42 $34 $42 $43 $42 $30 $42 $36 $42 $33 $42 $39 $42 $14 $9 $3 $5 $1 $2 $4 $7 $6 $8 $10 $11 $12 $13 $16 $399 $400 $410 $400 $401 $400 $402 $400 $403 $400 $404 $400 $405 $400 $406 $400 $407 $400 $408 $400 $409 $400 $24 $25 $INfile $OUTfile map local: Mapping|Map Translation|Map TITLE Map (GCG) INFO About Translation - Map (GCG) globalrules +36,+47,+19,+22,+27,+40,+1,+21,+13,+20 -36,-47,-19,-22,-27,-40,-1,-21,-13,-20 Main96 Main true 0 output biosequence/gcg prot? proenzyme.dat : enzyme.dat output Enzyme -DATa 90 No enzymes false !0 -ENZymes=# 36 false 9 false three forward frames !3,!4,!5,!6,!7,!8,!11 -MENu=t 10 false all six frames !3,!4,!5,!6,!7,!8,!11 -MENu=s 3 true frame 1 -MENu=a 4 true frame 2 -MENu=b 5 true frame 3 -MENu=c 6 true frame 4 -MENu=d 7 true frame 5 -MENu=e 8 true frame 6 -MENu=f 11 false open frames only 13 -MENu=o 12 false none !1,!21,!3,!4,!5,!6,!7,!8,!11 -MENu=n RSFFILE output biosequence/gcg map.rsf output Save Map cut sites as features in -RSF Optional97 Optional false 18 false Show enzymes that cut only once !14,!15 -ONCe 14 Minimum number of cuts 1, 1, 100000, 1 -MINCuts 15 Maximum number of cuts 100000, 1, 100000, 1 -MAXCuts 48 false Show enzymes with six or more bases in recognition site -SIXbase 170 Set minimum number of bases in recognition site false 17 17 Minimum site length 1, 1, 350, 1 -MINSitelen 47 false 37 5' overhang true -OVErhang=5 38 3' overhang true -OVErhang=3 39 blunt end true -OVErhang=0 16 Number of allowed mismatches 0, 0, 6, 1 -MISmatch 20 false Accept only perfect (non-ambiguous) matches !36 -PERFect 23 Suppress enzymes that cut within the region base1,base2 -EXClude 19 false Find "overlapping-set" matches -ALL 22 false Find translationally silent potential restriction sites -SILent 41 false 42 horizontally true 43 vertically false -MENu=VERtical 26 true Display a numbered scale line in the output -SCALeline 25 true Display the sequence in the output -SEQline 27 true Display the complement strand in the output -COMPline 40 false Display both forward and reverse strand cut positions -BOTtom 24 false Append the input data files to the output file -APPend 1 output biosequence/gcg translate.txt output Translation File -TRANSlate 21 false Use three letter amino acid symbols to display translations -THReeletter 13 Minimum open reading frame size 0, 0, 20000, 1 -OPEn 28 Lines per page 62, 18, 120, 1 -PAGe 29 Bases per line 60, 10, 110, 1 -WIDth 32 false Write a table of cut sites (instead of restriction map) 33,!36,!26,!25,!27,!1,!21,!13,!28,!29,!41 -TABle 33 false 34 cut position true 35 enzyme name (alphabetically) false -MENu=SORtbyenzyme 44 output biosequence/gcg name(SQ1+.cutters) output Write an enzyme data file with enzymes that did cut -CUTters 45 output biosequence/gcg name(SQ1+.noncutters) output Write an enzyme data file with enzymes that did not cut -NONCUTters 46 output biosequence/gcg name(SQ1+.excutters) output Write an enzyme data file with enzymes that were excluded -EXCUTters 30 Monitor program progress false -MONitor 31 Provide summary at the end of the program false -SUMmary HELP Help for Map http://sunflower.bio.indiana.edu/~gcg/genhelp/map.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}map $0 $90 $36 $9 $36 $10 $36 $3 $36 $4 $36 $5 $36 $6 $36 $7 $36 $8 $36 $11 $36 $12 $36 $RSFFILE $18 $14 $15 $48 $17 $47 $37 $47 $38 $47 $39 $47 $16 $20 $23 $19 $22 $41 $41 $43 $41 $26 $25 $27 $40 $24 $1 $21 $13 $28 $29 $32 $33 $33 $35 $33 $44 $45 $46 $30 $31 $INfile $OUTfile mapplot local: Mapping|MapPlot TITLE MapPlot (GCG) INFO About Mapping - MapPlot (GCG) globalrules +47,+12,+11,+10,+2 -47,-12,-11,-10,-2 Main98 Main true 1 output biosequence/gcg prot ? proenzyme.dat : enzyme.dat output Enzyme -DATa Optional99 Optional false 4 Show enzymes with six or more bases in the site false -SIXbase 5 Show enzymes that cut only once false !6,!7 -ONCe 6 Minimum number of cuts 1, 1, 100000, 1 -MINCuts 7 Maximum number of cuts 100000, 1, 100000, 1 -MAXCuts 170 Set minimum number of bases in recognition site false 19 19 Minimum site length 1, 1, 350, 1 -MINSitelen 47 false 37 5' overhang true -OVErhang=5 38 3' overhang true -OVErhang=3 39 blunt end true -OVErhang=0 9 Number of allowed mismatches 0, 0, 3, 1 -MISmatch 12 Accept only perfect (nonambiguous) matches false -PERFect 8 Suppress enzymes that cut within the region base1,base2 -EXCLude 11 Find "overlapping-set" matches false -ALL 10 Find translationally silent potential restriction sites false 2 -SILent 2 output biosequence/gcg translate.txt output Translation File -TRANSlate 15 output biosequence/gcg name(SQ1+.mapplot) output Make a text representation of the map, in file 17,18 -OUTfile 17 Append the enzyme file to the text file output false -APPend 18 Number of columns to use in text file output 45, 30, 100, 1 -WIDth 16 Plot true 3,14,9998 -PLOt 3 output biosequence/gcg output Mark File -MARk 9998 Set the plot density false 9999 9999 Number of bases per 100 platen units -DENsity 14 Number of platen units per line 1.6, 0.5, 10.0, 0.1 -SPAcing 44 output biosequence/gcg name(SQ1+.cutters) output Write an enzyme data file with enzymes that did cut -CUTters 45 output biosequence/gcg name(SQ1+.noncutters) output Write an enzyme data file with enzymes that did not cut -NONCUTters 46 output biosequence/gcg name(SQ1+.excutters) output Write an enzyme data file with enzymes that were excluded -EXCUTters HELP Help for MapPlot http://sunflower.bio.indiana.edu/~gcg/genhelp/mapplot.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}mapplot $1 $4 $5 $6 $7 $19 $47 $37 $47 $38 $47 $39 $47 $9 $12 $8 $11 $10 $2 $15 $17 $18 $16 $3 $9999 $14 $44 $45 $46 $INfile mapsort local: Mapping|MapSort TITLE MapSort (GCG) INFO About Mapping - MapSort (GCG) globalrules +8,+11,+10,+2,+47,+2 -8,-11,-10,-2,-47,-2 Main100 Main true 1 output biosequence/gcg prot ? proenzyme.dat : enzyme.dat output Enzyme -DATa Optional101 Optional false 3 Show enzymes with six or more bases in the recognition site false -SIXbase 4 Show enzymes that cut only once false !5,!6 -ONCe 5 Minimum number of cuts 1, 1, 100000, 1 -MINCuts 6 Maximum number of cuts 100000, 1, 100000, 1 -MAXCuts 170 Set minimum number of bases in recognition site false 17 17 Minimum site length 1, 1, 350, 1 -MINSitelen 47 false 37 5' overhang true -OVErhang=5 38 3' overhang true -OVErhang=3 39 blunt end true -OVErhang=0 7 Number of allowed mismatches 0, 0, 4, 1 -MISmatch 8 Accept only perfect (nonambiguous) matches false -PERFect 9 Suppress enzymes that cut within the region base1,base2 -EXCLude 11 Find "overlapping-set" matches false -ALL 10 Find translationally silent potential restriction sites false 2 -SILent 2 output biosequence/gcg translate.txt output Translation File -TRANSlate Optional102 Optional false HELP Help for MapSort http://sunflower.bio.indiana.edu/~gcg/genhelp/mapsort.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}mapsort $1 $3 $4 $5 $6 $17 $47 $37 $47 $38 $47 $39 $47 $7 $8 $9 $11 $10 $2 $INfile $OUTfile melttemp local: Nucleic|Primers|MeltTemp TITLE MeltTemp (GCG) INFO About Nucleic - Primers - MeltTemp (GCG) Main103 Main true 1 output biosequence/gcg output Oligo -PRImers Optional104 Optional false 2 output biosequence/gcg dnastack.dh output Enthalpies for DNA melting temperature determination -DATa1 3 output biosequence/gcg dnastack.ds output Entropies for DNA melting temperature determination -DATa2 4 Primer DNA concentration (nM) 50.0, .1, 500.0, 0.1 -DNAconcentration 5 Salt concentration (mM) 50.0, .1, 500.0, 0.1 -SALtconcentration HELP Help for MeltTemp http://sunflower.bio.indiana.edu/~gcg/genhelp/melttemp.html IOFiles Input/Output files false OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} ${callgcg}melttemp $1 $2 $3 $4 $5 $OUTfile1 meme local: Multiple Comparison|MEME Nucleic|Gene Finding|MEME TITLE MEME (GCG) INFO About Nucleic - Gene Finding - MEME (GCG) globalrules -222 +222 Main105 Main true MAKEREPORT Generate a report file true -REPort NMOTIFS Number of motifs to look for 6, 1, 16, 1 -NMOTifs MODELTYPE false OOPS Exactly one occurrence of each motif in each sequence false 222 -MODEL=ONEEXactly ZOOPS Zero or one occurrences of each motif in each sequence true -MODEL=ONEORZero ZOMPS Any # of occurrences of each motif in any sequence false -MODEL=ZEROORMore Optional106 Optional false 222 false 221 Search both strands false -MENu=TWOStrands 227 Search the top strand only false -MENu=NOTWOStrands MINWIDTH Minimum width of motifs to search for @MAXWIDTH 8, 8, 100, 1 -MINWidth MAXWIDTH Maximum width of motifs to search for 60, 0, 100, 1 -MAXWidth EMTHRESHOLD Convergence criterion for EM .001, 0.001, 0.1, 0.001 -EMTHReshold MAXEMITERATIONS Cut off EM after this many iterations 50, 1, 100, 1 -MAXEMiterations MONITOR Monitor search progress false -MONitor SUMMARY Print summary information to screen at exit false -SUMmary HELP Help for MEME http://sunflower.bio.indiana.edu/~gcg/genhelp/meme.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}meme $MAKEREPORT $NMOTIFS $MODELTYPE $OOPS $MODELTYPE $ZOOPS $MODELTYPE $ZOMPS $MODELTYPE $222 $221 $222 $227 $222 $MINWIDTH $MAXWIDTH $EMTHRESHOLD $MAXEMITERATIONS $MONITOR $SUMMARY mfold local: Nucleic|Secondary Structure|MFold TITLE MFold (GCG) INFO About Nucleic - Secondary Structure - MFold (GCG) Main107 Main true Optional108 Optional false 100 false 69 RNA true 70 DNA false -MENu=DNA @1,@2,@3,@4,@5,@6,@7,@8 701 Folding temperature (celsius) 37.0, 0.0, 100.0, .1 -TEMperature 9 Maximum size of interior loop 0, 0, 0, 1 -MAXLoopsize 10 Maximum lopsidedness of an interior loop 0, 0, 0, 1 -LOPsidedness Force k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to force k consecutive bases, beginning with i, to form base pairs. You may specify up to 9 of these regions. 60 i,j,k +61 -FORCe1 61 i,j,k +62 -FORCe2 62 i,j,k +63 -FORCe3 63 i,j,k +64 -FORCe4 64 i,j,k +65 -FORCe5 65 i,j,k +66 -FORCe6 66 i,j,k +67 -FORCe7 67 i,j,k +68 -FORCe8 68 i,j,k -FORCe9 Prevent k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to prevent k consecutive bases, beginning with i, from base pairing. You may specify up to 9 of these regions. 30 i,j,k +31 -PREVent1 31 i,j,k +32 -PREVent2 32 i,j,k +33 -PREVent3 33 i,j,k +34 -PREVent4 34 i,j,k +35 -PREVent5 35 i,j,k +36 -PREVent6 36 i,j,k +37 -PREVent7 37 i,j,k +38 -PREVent8 38 i,j,k -PREVent9 Exclude bases i+1 through j-1 from folding, forcing a base pair between i and j. You may specify up to 9 of these regions. 40 i,j +41 -CLOSedexcise1 41 i,j +42 -CLOSedexcise2 42 i,j +43 -CLOSedexcise3 43 i,j +44 -CLOSedexcise4 44 i,j +45 -CLOSedexcise5 45 i,j +46 -CLOSedexcise6 46 i,j +47 -CLOSedexcise7 47 i,j +48 -CLOSedexcise8 48 i,j -CLOSedexcise9 Exclude bases i through j from folding, ligating bases i-1 and j+1 together before folding. You may specify up to 9 of these regions. 50 i,j +51 -OPENexcise1 51 i,j +52 -OPENexcise2 52 i,j +53 -OPENexcise3 53 i,j +54 -OPENexcise4 54 i,j +55 -OPENexcise5 55 i,j +56 -OPENexcise6 56 i,j +57 -OPENexcise7 57 i,j +58 -OPENexcise8 58 i,j -OPENexcise9 8 #69 ? mfoldr037 : mfoldd037 Default file name extension for all local data files -EXTension 1 output biosequence/gcg output Energies for single base stacking -DATa1 2 output biosequence/gcg output Destabilizing energies for internal, bulge, and hairpin loops -DATa2 3 output biosequence/gcg output Energies for base stacking -DATa3 4 output biosequence/gcg output Energies for terminal mismatched pairs in hairpin loops -DATa4 5 output biosequence/gcg output Energies for terminal mismatched pairs in interior loops -DATa5 6 output biosequence/gcg output Bonus energies for recognized "tetraloops -DATa6 7 output biosequence/gcg output Energies for multi-branched and asymmetric interior loops -DATa7 17 Monitor program progress false -MONitor 18 Provide summary at the end of the program false -SUMmary HELP Help for MFold http://sunflower.bio.indiana.edu/~gcg/genhelp/mfold.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}mfold $100 $100 $70 $100 $701 $9 $10 $60 $61 $62 $63 $64 $65 $66 $67 $68 $30 $31 $32 $33 $34 $35 $36 $37 $38 $40 $41 $42 $43 $44 $45 $46 $47 $48 $50 $51 $52 $53 $54 $55 $56 $57 $58 $8 $1 $2 $3 $4 $5 $6 $7 $17 $18 $INfile $OUTfile mfold_2500 local: Uncataloged|mfold_2500 TITLE mfold_2500 (GCG) INFO About Uncataloged - mfold_2500 (GCG) Main109 Main true Optional110 Optional false 100 false 69 RNA true 70 DNA false -MENu=DNA @1,@2,@3,@4,@5,@6,@7,@8 701 Folding temperature (celsius) 37.0, 0.0, 100.0, .1 -TEMperature 9 Maximum size of interior loop 0, 0, 0, 1 -MAXLoopsize 10 Maximum lopsidedness of an interior loop 0, 0, 0, 1 -LOPsidedness Force k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to force k consecutive bases, beginning with i, to form base pairs. You may specify up to 9 of these regions. 60 i,j,k +61 -FORCe1 61 i,j,k +62 -FORCe2 62 i,j,k +63 -FORCe3 63 i,j,k +64 -FORCe4 64 i,j,k +65 -FORCe5 65 i,j,k +66 -FORCe6 66 i,j,k +67 -FORCe7 67 i,j,k +68 -FORCe8 68 i,j,k -FORCe9 Prevent k consecutive base pairs, starting with the base pair between i and j. Use i,0,k to prevent k consecutive bases, beginning with i, from base pairing. You may specify up to 9 of these regions. 30 i,j,k +31 -PREVent1 31 i,j,k +32 -PREVent2 32 i,j,k +33 -PREVent3 33 i,j,k +34 -PREVent4 34 i,j,k +35 -PREVent5 35 i,j,k +36 -PREVent6 36 i,j,k +37 -PREVent7 37 i,j,k +38 -PREVent8 38 i,j,k -PREVent9 Exclude bases i+1 through j-1 from folding, forcing a base pair between i and j. You may specify up to 9 of these regions. 40 i,j +41 -CLOSedexcise1 41 i,j +42 -CLOSedexcise2 42 i,j +43 -CLOSedexcise3 43 i,j +44 -CLOSedexcise4 44 i,j +45 -CLOSedexcise5 45 i,j +46 -CLOSedexcise6 46 i,j +47 -CLOSedexcise7 47 i,j +48 -CLOSedexcise8 48 i,j -CLOSedexcise9 Exclude bases i through j from folding, ligating bases i-1 and j+1 together before folding. You may specify up to 9 of these regions. 50 i,j +51 -OPENexcise1 51 i,j +52 -OPENexcise2 52 i,j +53 -OPENexcise3 53 i,j +54 -OPENexcise4 54 i,j +55 -OPENexcise5 55 i,j +56 -OPENexcise6 56 i,j +57 -OPENexcise7 57 i,j +58 -OPENexcise8 58 i,j -OPENexcise9 8 #69 ? mfoldr037 : mfoldd037 Default file name extension for all local data files -EXTension 1 output biosequence/gcg output Energies for single base stacking -DATa1 2 output biosequence/gcg output Destabilizing energies for internal, bulge, and hairpin loops -DATa2 3 output biosequence/gcg output Energies for base stacking -DATa3 4 output biosequence/gcg output Energies for terminal mismatched pairs in hairpin loops -DATa4 5 output biosequence/gcg output Energies for terminal mismatched pairs in interior loops -DATa5 6 output biosequence/gcg output Bonus energies for recognized "tetraloops -DATa6 7 output biosequence/gcg output Energies for multi-branched and asymmetric interior loops -DATa7 17 Monitor program progress false -MONitor 18 Provide summary at the end of the program false -SUMmary HELP Help for mfold_2500 http://sunflower.bio.indiana.edu/~gcg/genhelp/mfold_2500.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}mfold_2500 $100 $100 $70 $100 $701 $9 $10 $60 $61 $62 $63 $64 $65 $66 $67 $68 $30 $31 $32 $33 $34 $35 $36 $37 $38 $40 $41 $42 $43 $44 $45 $46 $47 $48 $50 $51 $52 $53 $54 $55 $56 $57 $58 $8 $1 $2 $3 $4 $5 $6 $7 $17 $18 $INfile $OUTfile moment local: Protein|Analysis|Moment TITLE Moment (GCG) INFO About Protein - Analysis - Moment (GCG) Main111 Main true 1 Number of contours to plot 2, 1, 10, 1 -NCONtours 0 Window size for averaging 10, 1, 40, 1 -WINdow Optional112 Optional false 2 Threshold for each contour\n(separate each with a comma) -CONTours 9998 Set the density false 9999 9999 Number of residues per page -DENsity 4 P Menu for plot -MENu HELP Help for Moment http://sunflower.bio.indiana.edu/~gcg/genhelp/moment.html IOFiles Input/Output files false INfile INfile ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}moment $1 $0 $2 $9999 $4 $INfile motifs local: Database|Sequence Search|Motifs Nucleic|Gene Finding|Motifs Protein|Analysis|Motifs TITLE Motifs (GCG) INFO About Protein - Analysis - Motifs (GCG) Main113 Main true 1 output biosequence/gcg prosite.patterns output Pattern -DATa 22 output biosequence/gcg motifs.rsf output Save results as features in file -RSF 23 output biosequence/gcg motifs.list output List file of output sequence names -LIStfile Optional114 Optional false 2 Include the PROSITE abstract for each pattern found true -REFerence 5 Write output file in list file format only false !2,!23 -NAMes 15 Append the pattern data file to your output file false !2 -APPend 3 false 31 search includes patterns that are frequently found in many proteins false -MENu=FREquent 32 search excludes patterns that are frequently found in many proteins true 12 false 13 report only motifs found in the sequence true 14 report all motifs searched false -MENu=SHOw 4 Number of allowed mismatches 0, 0, 5, 1 -MISmatch 6 Limit report to motifs found only once in the sequence false !7,!8 -ONCe 7 Minimum number of finds\nfor each motif 1, 0, 100000, 1 -MINCuts 8 Maximum number of finds\nfor each motif 100000, 1, 100000, 1 -MAXCuts 9 Do not report motifs found between positions residue1,residue2 -EXClude 10 Monitor sequences searched false -MONitor 11 Provide summary at the end of the program false -SUMmary HELP Help for Motifs http://sunflower.bio.indiana.edu/~gcg/genhelp/motifs.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}motifs $1 $22 $23 $2 $5 $15 $3 $31 $3 $3 $12 $12 $14 $12 $4 $6 $7 $8 $9 $10 $11 $INfile $OUTfile motifsearch local: Database|Sequence Search|MotifSearch TITLE MotifSearch (GCG) INFO About Database - Sequence Search - MotifSearch (GCG) Main115 Main true PROFILEFILE File with query profile(s) input biosequence/gcg input -INfile1 Optional116 Optional false LISTLIMIT Maximum number of entries\nin output list 10000, 1, 10000, 100 -LIStsize FRAGMENTS false Write aligned segments' Begin, End, Strand attributes -FRAGments HITTHRESHOLD Maximum allowable position pValue for\ndisplaying motif hits 0.0001, 0.000001, 0.1, 0.00001 -HITTHReshold MONITOR Monitor sequences searched at intervals of 100, 1, 2500, 1 -MONitor SUMMARY Print summary information to screen at exit false -SUMmary HELP Help for MotifSearch http://sunflower.bio.indiana.edu/~gcg/genhelp/motifsearch.html IOFiles Input/Output files false INfile2 INfile2 INfile2msf input biosequence/msf input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}motifsearch $PROFILEFILE $LISTLIMIT $FRAGMENTS $HITTHRESHOLD $MONITOR $SUMMARY $INfile2 $OUTfile mountains local: Uncataloged|mountains TITLE mountains (GCG) INFO About Uncataloged - mountains (GCG) Main117 Main true 20 Connect File input biosequence/gcg input -INfile Optional118 Optional false 2 Display the sequence false -SHOwseq 0 Set the number of stems on the Y axis of each page -STEMdepth 4 Draw ticks true 3 -TICks 3 Number the ticks true 200 -NUMbering 200 Set the tick number interval -NUMbering 9998 Set the density false 9999 9999 Number of bases per 100 platen units -DENsity HELP Help for mountains http://sunflower.bio.indiana.edu/~gcg/genhelp/mountains.html IOFiles Input/Output files false STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}mountains $20 $2 $0 $4 $3 $200 $9999 netblast local: Database|Sequence Search|NetBlast TITLE NetBlast (GCG) INFO About Database - Sequence Search - NetBlast (GCG) globalrules 9,+50 8,-50,-71 Main119 Main true 100 false 8 Search a protein database false @1,@9,@50 -MENu=DBProteinonly 9 Search a nucleotide database true @1,Prot?-71:(#8?-71:+71),Prot?-50:(#8?+50:-50) -MENu=DBNucleotideonly Optional120 Optional false 40 Filter input sequences for low complexity regions true -FILter 1000 Specify protein scoring matrix false +1010 1010 false 1001 BLOSUM45 false -MATRix=BLOSUM45 1002 BLOSUM62 true -MATRix=BLOSUM62 1003 BLOSUM80 false -MATRix=BLOSUM80 1004 PAM70 false -MATRix=PAM70 1005 PAM30 false -MATRix=PAM30 71 Translate query sequence false +50 -TBLASTX 50 false 51 Standard or Universal true -TRANSlate=1 52 Vertebrate Mitochondrial false -TRANSlate=2 53 Yeast Mitochondrial false -TRANSlate=3 54 Mold Mitochondrial and Mycoplasma false -TRANSlate=4 55 Invertebrate Mitochondrial false -TRANSlate=5 56 Ciliate Macronuclear false -TRANSlate=6 57 Echinodermate Mitochondrial false -TRANSlate=9 58 Alternative Ciliate Macronuclear false -TRANSlate=10 59 Eubacterial false -TRANSlate=11 501 Alternative Yeast false -TRANSlate=12 502 Ascidian Mitochondrial false -TRANSlate=13 503 Flatworm Mitochondrial false -TRANSlate=14 504 Blepharisma (ciliate) nuclear false -TRANSlate=15 505 Chlorophycean Mitochondrial false -TRANSlate=16 506 Trematode Mitochondrial false -TRANSlate=21 507 Scenedesmus obliquus Mitochondrial false -TRANSlate=22 508 Thraustochytrium Mitochondrial false -TRANSlate=23 2400 true Create gapped alignments 2401,2402 -GAPS 2401 Gap creation penalty (Zero selects default) -GAPweight 2402 Gap extension penalty (Zero selects default) -LENgthweight 20 Maximum number of sequence listed in the output 250, 0, 1000, 1 -LIStsize 37 Display alignments from how many sequences 100, 0, 1000, 1 -ALIgnments 34 Pass this string through to the BLAST command line -APPend HELP Help for NetBlast http://sunflower.bio.indiana.edu/~gcg/genhelp/netblast.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 1 ${callgcg}netblast $100 $8 $100 $9 $100 $40 $1010 $1001 $1010 $1002 $1010 $1003 $1010 $1004 $1010 $1005 $1010 $71 $50 $51 $50 $52 $50 $53 $50 $54 $50 $55 $50 $56 $50 $57 $50 $58 $50 $59 $50 $501 $50 $502 $50 $503 $50 $504 $50 $505 $50 $506 $50 $507 $50 $508 $50 $2400 $2401 $2402 $20 $37 $34 $INfile1 $INfile2 $OUTfile netfetch local: Database|Sequence Search|NetFetch TITLE NetFetch (GCG) INFO About Database - Sequence Search - NetFetch (GCG) Main121 Main true 30 Output file from NetBLAST input biosequence/gcg input -INfile Optional122 Optional false 17 Top number of sequences to request 0, 0, 1000, 1 -TOP 18 false Display program progress -MONitor 19 true Display summary information -SUMmary 20 false Keep response from NCBI in .raw file -RAW 23 Specify HTTP query if different from default -URL 24 false 25 Both true 26 Nucleotide false -TYPe=N 27 Protein false -TYPe=P HELP Help for NetFetch http://sunflower.bio.indiana.edu/~gcg/genhelp/netfetch.html IOFiles Input/Output files false INfile1 INfile1 INfile1msf input biosequence/msf input -INfile1=$value OUTfile1 OUTfile1 OUTfile1.txt output text/plain output -OUTfile1=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count -1 ${callgcg}netfetch $30 $17 $18 $19 $20 $23 $24 $24 $26 $24 $27 $24 $INfile1 $OUTfile1 nooverlap local: Multiple Comparison|NoOverlap TITLE NoOverlap (GCG) INFO About Multiple Comparison - NoOverlap (GCG) Main123 Main true 0 Length of words that must not occur @1 9, 1, 30, 1 -WORdsize 1 Minimum size of region with no common words 100, 0, 1000, 1 -MINlength Optional124 Optional false 3 Search only the top strand of the sequences false -ONEstrand 4 Monitor the progress with a screen trace false -MONitor 5 Include the summary at the end of the program false -SUMmary HELP Help for NoOverlap http://sunflower.bio.indiana.edu/~gcg/genhelp/nooverlap.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}nooverlap $0 $1 $3 $4 $5 $INfile1 $OUTfile olddistances local: Multiple Comparison|OldDistances TITLE OldDistances (GCG) INFO About Multiple Comparison - OldDistances (GCG) Main125 Main true 100 false 1 false length of the shorter sequence -MENu=1 2 true length of the shorter sequence without gaps -MENu=2 3 false average length -MENu=3 4 false average length without gaps -MENu=4 5 false nothing -MENu=5 6 Set minimum symbol comparison score for a match -THReshold 7 output biosequence/gcg Prot ? blosum62.cmp : dnadistances.cmp output Scoring Matrix -MATRix HELP Help for OldDistances http://sunflower.bio.indiana.edu/~gcg/genhelp/olddistances.html IOFiles Input/Output files false INfile INfile INfilegcg input biosequence/gcg input -INfile=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}olddistances $100 $1 $100 $2 $100 $3 $100 $4 $100 $5 $100 $6 $7 $INfile $OUTfile overlap local: Multiple Comparison|Overlap TITLE Overlap (GCG) INFO About Multiple Comparison - Overlap (GCG) Main126 Main true 100 false 20 same sequences true -WPIMENU=1 21 different sequences false 0 -WPIMENU=2 Optional127 Optional false 6 Upper limit on stringency 3.0, 0.0, 10.0, 0.1 -UPPERlimit HELP Help for Overlap http://sunflower.bio.indiana.edu/~gcg/genhelp/overlap.html IOFiles Input/Output files false INfile1 INfile1 INfile1gcg input biosequence/gcg input -INfile1=$value INfile2 INfile2 INfile2gcg input biosequence/gcg input -INfile2=$value OUTfile OUTfile OUTfile.txt output text/plain output -OUTfile=$value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} InputSequenceCount Input sequence count 3 ${callgcg}overlap $100 $20 $100 $21 $100 $6 $INfile1 $INfile2 $OUTfile paupdisplay local: Phylogeny|PaupDisplay TITLE PaupDisplay (GCG) INFO About Phylogeny - PaupDisplay (GCG) Main128 Main true 0 Trees file from PAUPSearch input biosequence/gcg input -INfile 1 false