#----------------------- FASTA (DNA/RNA) ( 4/17/98) ----------------------
# If environment variable $THREADED is set to _t, the threaded versions
# of fasta programs will be used. This is conveniently done in 
# your .cshrc file 'setenv THREADED _t'. 
item:FASTA (DNA/RNA vs. DNA database)
itemmethod:(readseq -a -f8 in1 > infile.fasta; nice $PROGRAM$THREADED -Q -d $NUMOFALN $MARKX infile.fasta $DBASE $KTUP > in1.out; fastaout.csh $MARKX in1.out $WHERE; rm infile.fasta in1) &
itemhelp: FASTA/fasta.asc

in:in1
informat:genbank
inmask:
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:HIV-1 Seq. Db.:/var/www/cgi-bin/db/hiv17-08-01.fasta2
argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta
argchoice:HIV-1 HXB2 Numbering:/var/www/cgi-bin/db/HXB2.fasta
argchoice:HCV Numbering:/var/www/cgi-bin/db/HCV.fasta
argchoice:GenBank Primate:@$DAT/fasta/gbpri.fil
argchoice:GenBank Rodent:$GB/gbrod.wrp
argchoice:GenBank all Mammal:$GB/gbmam.wrp
argchoice:GenBank verteBrates:$GB/gbvrt.wrp
argchoice:GenBank Inverts:$GB/gbinv.wrp
argchoice:GenBank pLants:$GB/gbpln.wrp
argchoice:GenBank Struct RNA:$GB/gbrna.wrp
argchoice:GenBank Expressed Sequence Tags:@$DAT/fasta/gbest.fil
argchoice:GenBank phaGe:$GB/gbphg.wrp
argchoice:GenBank bacTeria:$GB/gbbct.wrp
argchoice:GenBank sYnthetic:$GB/gbsyn.wrp
argchoice:GenBank Viral:$GB/gbvrl.wrp
argchoice:GenBank Unannotated:$GB/gbuna.wrp
argchoice:GenBank Patented:$GB/gbpat.wrp
argchoice:GenBank Seq. Tagged Sites:$GB/gbsts.wrp
argchoice:GenBank High Throughput Genomic:$GB/gbhtg.wrp
argchoice:GenBank Genome Survey Seq.:$GB/gbgss.wrp
argchoice:VecBase vector database:$VEC/vecbase.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:PROGRAM
argtype:choice_menu
argchoice:fasta - quick, sensitive:fasta33
argchoice:ssearch - SLOW!, exhaustive:ssearch33
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:6
argvalue:4

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit windows: 
argchoice:Output file:$OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

#-------------------------- fasta (protein)  ( 4/18/98) ----------------------
# If environment variable $THREADED is set to _t, the threaded versions
# of fasta programs will be used. This is conveniently done in 
# your .cshrc file 'setenv THREADED _t'. 
item:FASTA (protein vs. protein database)
itemmethod:(readseq -a -f8 in1 > infile.fasta;nice $PROGRAM$THREADED -Q -d $NUMOFALN $MARKX $MATRIX infile.fasta $DBASE $KTUP > in1.out; fastaout.csh $MARKX in1.out $WHERE; rm in1*) &
itemhelp: FASTA/fasta.asc

in:in1
informat:genbank
inmask:
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:SIV:/database/AA/SIVENVPRO.fasta
argchoice:GenPept:$GENPEPT/genpept.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:PROGRAM
argtype:choice_menu
argchoice:fasta - (quick, sensitive):fasta33
argchoice:ssearch - (SLOW!, exhaustive):ssearch33
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:Blosum50 (Protein default):-s $dat/fasta/blosum50.mat
argchoice:Blosum45:-s $dat/fasta/blosum45.mat
argchoice:Blosum62:-s $dat/fasta/blosum62.mat
argchoice:MD20:-s $dat/fasta/md_20.mat
argchoice:PAM120 (Protein):-s $dat/fasta/pam120.mat
argchoice:PAM250 (Protein):-s $dat/fasta/pam250.mat
argchoice:PAM250, Gonnet et al. (Protein):-s $dat/fasta/gonnet.mat
argchoice:Genetic Code Matrix (Protein):-s $dat/fasta/codaa.mat
argchoice:Weight Diagonals Only (Protein):-s $dat/fasta/altdiag.mat
argchoice:Lipman Alt.Matrix (Protein):-s $dat/fasta/altprot.mat
argchoice:Identity Matrix (Protein):-s $dat/fasta/idnaa.mat
argchoice:Weighted Identity Matrix (Protein):-s $dat/fasta/idpaa.mat
argvalue:0

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit windows: 
argchoice:Output file:$OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

#-------------------------- fastx/y (protein)  ( 4/18/98) ----------------------
# If environment variable $THREADED is set to _t, the threaded versions
# of fasta programs will be used. This is conveniently done in 
# your .cshrc file 'setenv THREADED _t'. 
item:FASTA (cDNA vs. protein database)
itemmethod:(readseq -a -f8 in1 > infile.fasta;nice $PROGRAM$THREADED -Q -d $NUMOFALN $MARKX $MATRIX infile.fasta $DBASE $KTUP > in1.out; fastaout.csh $MARKX in1.out $WHERE; rm in1*) &
itemhelp: FASTA/fasta.asc

in:in1
informat:genbank
inmask:
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:SIV:/database/AA/SIVENVPRO.fasta
argchoice:GenPept:$GENPEPT/genpept.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:Allow gaps
argtype:choice_menu
argchoice:fastx - between codons only (faster):fastx33
argchoice:fasty - WITHIN codons (sensitive):fasty33
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:Blosum50 (Protein default):-s $dat/fasta/blosum50.mat
argchoice:Blosum45:-s $dat/fasta/blosum45.mat
argchoice:Blosum62:-s $dat/fasta/blosum62.mat
argchoice:MD20:-s $dat/fasta/md_20.mat
argchoice:PAM120 (Protein):-s $dat/fasta/pam120.mat
argchoice:PAM250 (Protein):-s $dat/fasta/pam250.mat
argchoice:PAM250, Gonnet et al. (Protein):-s $dat/fasta/gonnet.mat
argchoice:Genetic Code Matrix (Protein):-s $dat/fasta/codaa.mat
argchoice:Weight Diagonals Only (Protein):-s $dat/fasta/altdiag.mat
argchoice:Lipman Alt.Matrix (Protein):-s $dat/fasta/altprot.mat
argchoice:Identity Matrix (Protein):-s $dat/fasta/idnaa.mat
argchoice:Weighted Identity Matrix (Protein):-s $dat/fasta/idpaa.mat
argvalue:0

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit windows: 
argchoice:Output file:$OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

#----------------------- tfasta (protein) ( 4/15/98) -----------------------
item:TFASTA (Protein vs. DNA Database, Translated in 6 Reading Frames)
itemmethod:(readseq -a -f8 in1 > infile.tfasta;nice $PROGRAM$THREADED -Q -d $NUMOFALN $MARKX $MATRIX infile.tfasta $DBASE $KTUP $FRAMES > in1.out; fastaout.csh $MARKX in1.out $WHERE; rm in1*) &
itemhelp: FASTA/fasta.asc

in:in1
informat:genbank
inmask:
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:HIV-1 Seq. Db.:/var/www/cgi-bin/db/hiv17-08-01.fasta2
argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta
argchoice:HIV-1 HXB2 Numbering:/var/www/cgi-bin/db/HXB2.fasta
argchoice:HCV Numbering:/var/www/cgi-bin/db/HCV.fasta
argchoice:GenBank Primate:@$DAT/fasta/gbpri.fil
argchoice:GenBank Rodent:$GB/gbrod.wrp
argchoice:GenBank all Mammal:$GB/gbmam.wrp
argchoice:GenBank verteBrates:$GB/gbvrt.wrp
argchoice:GenBank Inverts:$GB/gbinv.wrp
argchoice:GenBank pLants:$GB/gbpln.wrp
argchoice:GenBank Struct RNA:$GB/gbrna.wrp
argchoice:GenBank Expressed Sequence Tags:@$DAT/fasta/gbest.fil
argchoice:GenBank phaGe:$GB/gbphg.wrp
argchoice:GenBank bacTeria:$GB/gbbct.wrp
argchoice:GenBank sYnthetic:$GB/gbsyn.wrp
argchoice:GenBank Viral:$GB/gbvrl.wrp
argchoice:GenBank Unannotated:$GB/gbuna.wrp
argchoice:GenBank Patented:$GB/gbpat.wrp
argchoice:GenBank Seq. Tagged Sites:$GB/gbsts.wrp
argchoice:GenBank High Throughput Genomic:$GB/gbhtg.wrp
argchoice:GenBank Genome Survey Seq.:$GB/gbgss.wrp
argchoice:VecBase vector database:$VEC/vecbase.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:Allow gaps
argtype:choice_menu
argchoice:tfasta - none:tfasta33
argchoice:tfastx - between codons only (faster):tfastx33
argchoice:tfasty - WITHIN codons (sensitive):tfasty33
argvalue:0

arg:FRAMES
arglabel:Translate
argtype:chooser
argchoice:3 frames:-3
argchoice:6 frames:
argvalue:1

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:Blosum50 (Protein default):-s $dat/fasta/blosum50.mat
argchoice:Blosum45:-s $dat/fasta/blosum45.mat
argchoice:Blosum62:-s $dat/fasta/blosum62.mat
argchoice:MD20:-s $dat/fasta/md_20.mat
argchoice:PAM120 (Protein):-s $dat/fasta/pam120.mat
argchoice:PAM250 (Protein):-s $dat/fasta/pam250.mat
argchoice:PAM250, Gonnet et al. (Protein):-s $dat/fasta/gonnet.mat
argchoice:Genetic Code Matrix (Protein):-s $dat/fasta/codaa.mat
argchoice:Weight Diagonals Only (Protein):-s $dat/fasta/altdiag.mat
argchoice:Lipman Alt.Matrix (Protein):-s $dat/fasta/altprot.mat
argchoice:Identity Matrix (Protein):-s $dat/fasta/idnaa.mat
argchoice:Weighted Identity Matrix (Protein):-s $dat/fasta/idpaa.mat
argvalue:0

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit windows: 
argchoice:Output file:$OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text