fasta_3.4(t25d6).yaml

!mobyle/program
name: fasta
version: 3.4(t25d6)
title: FASTA
description: Sequence database search
authors: W. Pearson
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: '- fasta: scan a protein or DNA sequence library for similar sequences-
            tfasta: compare a protein sequence to a DNA sequence librarSy, translating
            the DNA sequence library `on-the-fly'' to the 3 forward and the 3 reverse
            frames without frameshifts.- fastx/fasty: compare a DNA sequence to a
            protein sequence database, comparing the translated DNA sequence in three
            frames, with frameshifts. fasty2 allows frameshifts inside codons.- tfastx/tfasty:
            compare a protein sequence vs a translated DNA db, with frameshifts. tfasty
            allows frameshifts inside codons.- fastf/tfastf: compare an ordered peptide
            mixture (obtained for example by Edman degradation of a CNBr cleavage)
            against a protein or translated DNA database.- fasts/tfasts: compare a
            set of short peptide fragments (obtained from a mass-spec analysis of
            a protein) against a protein or translated DNA database.'
        prompt: Fasta program
        format: str(value) + " -q"
        simple: true
        argpos: 0
        mandatory: true
        name: fasta
        command: true
        type: !mobyle/stringtype
            default: 'null'
            options:
            - {label: Choose a program, value: 'null'}
            - {label: fasta (protein or nucleotide query vs similar db ), value: fasta}
            - {label: tfasta (protein query vs translated nucleic db), value: tfasta}
            - {label: fastx (translated nucleotide query  vs protein db (frameshifts
                    only only between codons)), value: fastx}
            - {label: tfastx (protein query vs translated DNA db (frameshifts only
                    between codons)), value: tfastx}
            - {label: fasty (fastx + frameshifts anywhere), value: fasty}
            - {label: tfasty (tfastx + frameshifts anywhere), value: tfasty}
            - {label: fastf (mixed peptide seq vs protein db (modified algorithm)),
                value: fastf}
            - {label: tfastf (mixed peptide seq vs translated DNA db (modified algorithm)),
                value: tfastf}
            - {label: fasts (several short peptide seq vs protein db (modified algorithm)),
                value: fasts}
            - {label: tfasts (several short peptide seq vs translated DNA db (modified
                    algorithm)), value: tfasts}
    - !mobyle/inputprogramparameter
        prompt: Query sequence File
        format: '" "+str(value)'
        simple: true
        argpos: 2
        mandatory: true
        name: query
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        prompt: Is it a DNA or protein sequence (-n)
        format: ( "" , " -n" )[ value is not None and value == "DNA" and fasta ==
            'fasta']
        simple: true
        argpos: 1
        mandatory: true
        name: seqtype
        command: false
        type: !mobyle/stringtype
            default: 'null'
            options:
            - {label: Choose a biotype, value: 'null'}
            - {label: DNA, value: DNA}
            - {label: Protein, value: protein}
    - !mobyle/inputprogramparagraph
        prompt: Database
        name: db
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            comment: Choose a protein db for fasta, fastx, fatsf, fasty or fasts.Please
                note that Swissprot usage by and for commercial entities requires
                a license agreement.
            prompt: Protein Database
            format: '" /path/to/fasta/databank/dir/" + str(value)'
            simple: true
            mandatory: true
            name: protein_db
            precond:
                '#or':
                -   '#and':
                    - {seqtype: protein}
                    - {fasta: fasta}
                -   fasta:
                        '#in': [fastx, fasty, fastf, fasts]
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a database, value: 'null'}
                - {label: 'uniprot: Universal Protein Resource', value: uniprot}
                - {label: 'uniprot_sprot: Universal Protein Resource (SwissProt part)',
                    value: uniprot_sprot}
                - {label: 'uniprot_trembl: Universal Protein Resource (TrEmbl part)',
                    value: uniprot_trembl}
                - {label: 'nrprot: NCBI non-redundant Genbank CDS translations+PDB+Swissprot+PIR',
                    value: nrprot}
                - {label: 'nrprot_month: NCBI month non-redundant Genbank CDS translations+PDB+Swissprot+PIR',
                    value: nrprot_month}
                - {label: 'genpept: Genbank translations (last rel. + upd.)', value: genpept}
                - {label: 'genpept_new: genpept updates', value: genpept_new}
                - {label: 'gpbct: genpept bacteries', value: gpbct}
                - {label: 'gppri: primates', value: gppri}
                - {label: 'gpmam: other mammals', value: gpmam}
                - {label: 'gprod: rodents', value: gprod}
                - {label: 'gpvrt: other vertebrates', value: gpvrt}
                - {label: 'gpinv: invertebrates', value: gpinv}
                - {label: 'gppln: plants (including yeast)', value: gppln}
                - {label: 'gpvrl: virus', value: gpvrl}
                - {label: 'gpphg: phages', value: gpphg}
                - {label: 'gpsts: STS', value: gpsts}
                - {label: 'gpsyn: synthetic', value: gpsyn}
                - {label: 'gppat: patented', value: gppat}
                - {label: 'gpuna: unatotated', value: gpuna}
                - {label: 'gphtg: GS (high throughput Genomic Sequencing)', value: gphtg}
                - {label: 'sbase: annotated domains sequences', value: sbase}
        - !mobyle/inputprogramparameter
            comment: Choose a nucleotide db for fasta, tfasta, tfastx, tfasty, tfastf
                or tfasts
            prompt: Nucleotid Database
            format: '" /path/to/fasta/databank/dir/" + str(value)'
            simple: true
            mandatory: true
            name: nucleotid_db
            precond:
                '#or':
                -   '#and':
                    - {seqtype: DNA}
                    - {fasta: fasta}
                -   fasta:
                        '#in': [tfasta, tfastx, tfasty, tfastf, tfasts]
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a database, value: 'null'}
                - {label: 'embl: Embl last release + updates', value: embl}
                - {label: 'embl_new: Embl updates', value: embl_new}
                - {label: 'genbank: Genbank last release + updates', value: genbank}
                - {label: 'genbank_new: Genbank updates', value: genbank_new}
                - {label: 'gbbct: genbank bacteria', value: gbbct}
                - {label: 'gbpri: primates', value: gbpri}
                - {label: 'gbmam: other mammals', value: gbmam}
                - {label: 'gbrod: rodents', value: gbrod}
                - {label: 'gbvrt: other vertebrates', value: gbvrt}
                - {label: 'gbinv: invertebrates', value: gbinv}
                - {label: 'gbpln: plants (including yeast)', value: gbpln}
                - {label: 'gbvrl: virus', value: gbvrl}
                - {label: 'gbphg: phages', value: gbphg}
                - {label: 'gbest: EST (Expressed Sequence Tags)', value: gbest}
                - {label: 'gbsts: STS (Sequence Tagged sites)', value: gbsts}
                - {label: 'gbsyn: synthetic', value: gbsyn}
                - {label: 'gbpat: patented', value: gbpat}
                - {label: 'gbuna: unannotated', value: gbuna}
                - {label: 'gbgss: Genome Survey Sequences', value: gbgss}
                - {label: 'gbhtg: GS (high throughput Genomic Sequencing)', value: gbhtg}
                - {label: 'imgt: IMGT/LIGM-DB, ImMunoGeneTics sequence database',
                    value: imgt}
                - {label: 'borrelia: Borrelia burgdorferi complete genome', value: borrelia}
                - {label: 'ecoli: Escherichia Coli complete genome', value: ecoli}
                - {label: 'genitalium: Mycoplasma Genitalium complete genome', value: genitalium}
                - {label: 'pneumoniae: Mycoplasma Pneumoniae complete genome', value: pneumoniae}
                - {label: 'hpylori: Helicobacter Pylori complete genome', value: hpylori}
                - {label: 'bsubtilis: Bacillus Subtilis complete genome', value: bsubtilis}
                - {label: 'tuberculosis: Mycobacterium tuberculosis complete genome',
                    value: tuberculosis}
                - {label: 'ypestis: Yersinia pestis unfinished genome', value: ypestis}
                - {label: 'yeast: Yeast chromosomes', value: yeast}
                - {label: 'pfalciparum: Plasmodium falciparum 3D7', value: pfalciparum}
        - !mobyle/inputprogramparameter
            comment: Break long library sequences into blocks of N residues.  Useful
                for bacterial genomes, which have only one sequence entry.  -N 2000
                works well for well for bacterial genomes.
            prompt: Break long library sequences into blocks (-N)
            format: ( "" , " -N " + str(value) )[ value is not None ]
            name: break_long
            command: false
            type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Selectivity options
        name: selectivity_opt
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            comment: ktup sets the sensitivity and speed of the search. If ktup=2,
                similar regions in the two sequences being compared are found by looking
                at pairs of aligned residues; if ktup=1, single aligned amino acids
                are examined. ktup can be set to 2 or 1 for protein sequences, or
                from 1 to 6 for DNA sequences. The default if ktup is not specified
                is 2 for proteins and 6 for DNA. 1ktup=1 should be used for oligonucleotides
                (DNA query length < 20).
            prompt: Sensitivity and speed of the search
            format: ("" , " " + str(value) )[ value is not None ]
            argpos: 4
            name: ktup
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: The threshold value is normally calculated based on sequence
                length.
            prompt: Threshold for band optimization (FASTA, FASTX). (-c)
            format: ("" , " -c " + str(value) )[ value is not None ]
            name: optcut
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: The default for fasta with proteins is -12 and -16 for DNAThe
                default for fastx/fasty/tfastz/tfasty is -15.
            prompt: Penalty for opening a gap (-f)
            format: ("" , " -f " + str(value))[ value is not None ]
            name: gapinit
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: The default for fasta is -2 for proteins and -4 for DNAThe default
                for fastx/fasty/tfastz/tfasty is -3.
            prompt: Penalty for gap extension (-g)
            format: ("" , " -g " + str(value))[ value is not None ]
            name: gapext
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Expectation value limit for displaying scores and alignments.
                Defaults  are 10.0 for FASTA  protein searches, 5.0 for translated
                DNA/protein comparisons, and 2.0 for DNA/DNA searches.
            prompt: Maximal expectation value threshold for displaying scores and
                alignments (-E)
            format: ("" , " -E " + str(value))[ value is not None and value != vdef]
            name: high_expect
            command: false
            type: !mobyle/floattype {default: 10.0}
        - !mobyle/inputprogramparameter
            comment: Expectation value lower limit for score and alignment display.  If
                value is 1e-6  prevents library sequences with E()-values lower than
                1e-6 from being displayed. This allows the use to focus on more distant
                relationships.This allow one to skip over close relationships in searches
                for more distant relationships.
            prompt: Minimal expectation value threshold for displaying scores and
                alignments (-F)
            format: ("" , " -F  " + str(value))[ value is not None ]
            name: low_expect
            command: false
            type: !mobyle/floattype {}
    - !mobyle/inputprogramparagraph
        prompt: Scoring options
        name: score_opt
        argpos: 1
        children:
        - !mobyle/inputprogramparagraph
            prompt: Nucleic penalty
            name: scoring_nucleic
            precond:
                '#and':
                - {fasta: fasta}
                - {seqtype: DNA}
            children:
            - !mobyle/inputprogramparameter
                prompt: Maximum positive value for a nucleotid match (-r)
                name: nucleotid_match
                command: false
                type: !mobyle/integertype {default: 5}
            - !mobyle/inputprogramparameter
                comment: '''+5/-4'' are the default values for nucleotid match/mismatch,
                    but ''+3/-2'' can perform better in some cases.'
                prompt: Maximum negative penalty value for a nucleotid mismatch (-r)
                format: ( "" , ' -r "' + str(nucleotid_match) + '/' + str(value)+
                    '"' )[ value is not None and nucleotid_match is not None and (nucleotid_match
                    != 5 and value != vdef) ]
                name: nucleotid_mismatch
                precond:
                    nucleotid_match: {'#ne': None}
                command: false
                type: !mobyle/integertype {default: -4}
        - !mobyle/inputprogramparagraph
            prompt: Protein penalty
            name: scoring_protein
            precond:
                seqtype: {'#ne': DNA}
            children:
            - !mobyle/inputprogramparameter
                prompt: Scoring matrix file (-s)
                format: ( "" , " -s  " + str(value) )[ value is not None and value
                    != vdef]
                name: matrix
                command: false
                type: !mobyle/stringtype
                    default: BL50
                    options:
                    - {label: BLOSUM50, value: BL50}
                    - {label: BLOSUM62, value: BL62}
                    - {label: BLOSUM80, value: BL80}
                    - {label: PAM20, value: P20}
                    - {label: PAM40, value: P40}
                    - {label: PAM120, value: P120}
                    - {label: PAM250, value: P250}
                    - {label: MDM_10, value: M10}
                    - {label: MDM_20, value: M20}
                    - {label: MDM_40, value: M40}
            - !mobyle/inputprogramparameter
                comment: Particularly useful for fast[xy], where termination codons
                    are encoded as 'X'.
                prompt: Penalty for a match to 'X' (independently of the PAM matrix)
                    (-x)
                format: ( "" , " -x  " + str(value) )[ value is not None ]
                name: X_penalty
                command: false
                type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Frameshift and translation options
        name: frame_transl_opt
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            prompt: Penalty for frameshift between two codons (fast[xy]/tfast[xy])
                (-h)
            format: ("" , " -h  " + str(value))[ value is not None ]
            name: frameshift
            precond:
                fasta:
                    '#in': [fastx, fasty, tfastx, tfasty]
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Penalty for frameshift within a codon (fasty/tfasty) (-j)
            format: ("" , " -j  " + str(value))[ value is not None ]
            name: frameshift_within
            precond:
                fasta:
                    '#in': [fasty, tfasty]
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Search only the three forward frames (-3)
            format: ("" , " -3")[ value ]
            name: threeframe
            precond:
                fasta:
                    '#in': [tfasta, tfastx, tfasty]
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Reverse complement the query sequence (-i)
            format: ( "" , " -i" )[ value ]
            name: invert
            precond:
                fasta:
                    '#in': [fastx, tfastx, fasty, tfasty]
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)
            format: ( "" , " -t  " + str(value) )[ value is not None and value !=
                vdef]
            name: genetic_code
            precond:
                fasta:
                    '#in': [tfasta, tfastx, tfasty, tfastf, tfasts, fastx, fasty]
            command: false
            type: !mobyle/stringtype
                default: '1'
                options:
                - {label: Standard (1), value: '1'}
                - {label: Vertebrate Mitochondrial (1), value: '2'}
                - {label: Yeast Mitochondrial (2), value: '3'}
                - {label: 'Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
                        (3)', value: '4'}
                - {label: Invertebrate Mitochondrial (4), value: '5'}
                - {label: Ciliate Macronuclear and Dasycladacean (5), value: '6'}
                - {label: Echinoderm Mitochondrial (6), value: '9'}
                - {label: Euplotid Nuclear (7), value: '10'}
                - {label: Bacterial (8), value: '11'}
                - {label: Alternative Yeast Nuclear (9), value: '12'}
                - {label: Ascidian Mitochondrial (10), value: '13'}
                - {label: Flatworm Mitochondrial (11), value: '14'}
                - {label: Blepharisma Macronuclear (12), value: '15'}
    - !mobyle/inputprogramparagraph
        prompt: Optimization options
        name: optimize_opt
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            comment: Set the band-width used for optimization. -y 16 is the default
                for protein when ktup=2 and for all DNA alignments. -y 32 is used
                for protein and ktup=1. For proteins, optimization slows comparison
                2-fold and is highly recommended.
            prompt: Band-width used for optimization (-y)
            format: ("" , " -y  " + str(value))[ value is not None ]
            name: band
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Force Smith-Waterman alignment for output. Smith-Waterman is
                the default for protein sequences and FASTX, but not for TFASTA or
                DNA comparisons with FASTA.
            prompt: Force Smith-Waterman alignment for DNA (-A)
            format: ("" , " -A")[ value ]
            name: swalig
            precond:
                '#and':
                -   fasta:
                        '#in': [tfasta, fasta]
                - {seqtype: DNA}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Turn off default optimization of all scores greater than OPTCUT.
                Shirt results by 'initn' scores reduces the accuracy of statistical
                estimates. This was  the behavior of fasta1 versions.
            prompt: Turn fasta band optimization off during initial phase (-o)
            format: ("" , " -o")[ value ]
            name: noopt
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: In general, 1 and 2 are the best methods.
            prompt: Specify statistical calculation. (-z)
            format: ( (( "", " -z  " + str(value) )  [ value is not None and value
                != vdef]) , " -z 1" + str(value) )[value is not None and value > 0
                and random is not None ]
            name: stat
            command: false
            type: !mobyle/stringtype
                default: '1'
                options:
                - {label: Turn off statistics (0), value: '0'}
                - {label: Weigthed regression against the length of the library sequence
                        (1), value: '1'}
                - {label: Maximum likelihood estimates of Lambda abd K (2), value: '2'}
                - {label: Altschul-Gishas statistical (3), value: '3'}
                - {label: 'Alternate regression method: Variation 1 of 1 (4)', value: '4'}
                - {label: 'Alternate regression method: Variation 2 of 1 (5)', value: '5'}
                - {label: Maximum likelihood estimate based on the method of Mott
                        (6), value: '6'}
        - !mobyle/inputprogramparameter
            comment: This doubles the time required for a search, but allows accurate
                statistics to be estimated for libraries comprised of a single protein
                family.
            prompt: Estimate statistical parameters from shuffled copies of each library
                sequence (-z)
            name: random
            precond:
                stat: {'#gt': '0'}
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Report options
        name: affichage
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            prompt: Turn off histogram display (-H)
            format: ("" , " -H" )[ value ]
            name: histogram
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Number of similarity scores to be shown (-b)
            format: (""  , " -b "  + str(value))[ value is not None and value <= high_expect]
            name: scores
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Number of alignments to be shown (-d)
            format: ("" , " -d  " + str(value))[ value is not None and value <= high_expect]
            name: alns
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: HTML output (-m)
            format: ( ""  , " -m 6" )[ value ]
            simple: true
            name: html_output
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: (MARKX) =0,1,2,3,4. Alternate display of matches and mismatches
                in alignments.MARKX=0 uses ':','.',' ', for identities, conservative
                replacements, and non-conservative replacements, respectively.MARKX=1
                uses ' ','x', and 'X'.MARKX=2 does not show the second sequence, but
                uses the second alignment line to display matches with a '.' for identity,
                or with the mismatched residue for mismatches. MARKX=2 is useful for
                aligning large numbers of similar sequences.MARKX=3 writes out a file
                of library sequences in FASTA format. MARKX=3 should always be used
                with the 'SHOWALL' (-a) option, but this does not completely ensure
                that all of the sequences output will be aligned.MARKX=4 displays
                a graph of the alignment of the library sequence with respect to the
                query sequence, so that one can identify the regions of the query
                sequence that are conserved.
            prompt: Alternate display of matches and mismatches in alignments (-m)
            format: ( ""  , " -m  " + str(value) )[ value is not None and value !=
                vdef]
            name: markx
            precond: {'#not': html_output}
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: '0 [: identities] [. conservative repl] [ non-conserv repl]',
                    value: '0'}
                - {label: '1: [ identities] [x conservative repl] [X non-conserv repl]',
                    value: '1'}
                - {label: '2: [. identities] [res mismatch] - don''t display the 2nd
                        seq', value: '2'}
                - {label: '3: writes a file of library sequences in FASTA format',
                    value: '3'}
                - {label: '4: displays a graph of the alignment', value: '4'}
                - {label: '9: 0 + percent identity + coordinates', value: '9'}
                - {label: '10: output more information', value: '10'}
        - !mobyle/inputprogramparameter
            prompt: Sequences ranked by the z-score based on the init1 score (-1)
            format: ("" , " -1")[ value ]
            name: init1
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Show normalize score as (-B)
            format: ( "" , " -B" )[ value is not None and value != vdef]
            name: z_score_out
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: z-score (1), value: '1'}
                - {label: bit-score (0), value: '0'}
        - !mobyle/inputprogramparameter
            prompt: Output line length for sequence alignments (-w)
            format: ("" , " -w  " + str(value))[ value is not None and value != vdef
                ]
            name: linlen
            command: false
            type: !mobyle/integertype {default: 60}
        - !mobyle/inputprogramparameter
            comment: Causes fasta/lfasta/plfasta to start numbering the aligned sequences
                starting with offset1 and offset2, rather than 1 and 1. This is particularly
                useful for showing alignments of promoter regions.
            prompt: Start numbering the aligned sequences at position x1 x2 (2 numbers
                separated by comma) (-X)
            format: ("" , ' -X "' +  str(value) + '"')[ value is not None ]
            name: offsets
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Display more information about the library sequence in the alignment
                (-L)
            format: ("" , " -L")[ value ]
            name: info
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Other options
        name: other_opt
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            comment: Treat lower-case characters in the query or library sequence
                as 'low-complexity' residues. These characters are treated as 'X'
                during the initial scan, but are treated as normal residues during
                the final alignment. Sinces statistical significance is calculated
                from similarity score calculated during library search, low complexity
                regions will not produce statistical significant matches.If a significant
                alignment contains low complexity regions the final score may be higher
                than the score obtained during the search.
            prompt: Lower case filtering (-S)
            format: ( "" , " -S" )[ value ]
            name: filter
            command: false
            type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Fasta report
        filenames: '"fasta.out"'
        name: outfile
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Html output file
        filenames: '"fasta.html"'
        argpos: 100
        name: html_outfile
        precond: html_output
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"fasta.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: 'Pearson, W. R. (1999) Flexible sequence similarity searching
        with the FASTA3 program package. Methods in Molecular Biology', url: null}
- {doi: null, label: 'W. R. Pearson and D. J. Lipman (1988), Improved Tools for Biological
        Sequence Analysis, PNAS 85:2444-2448', url: null}
- {doi: null, label: 'W. R. Pearson (1998) Empirical statistical estimates for sequence
        similarity searches. In J. Mol. Biol. 276:71-84', url: null}
- {doi: null, label: 'Pearson, W. R. (1996) Effective protein sequence comparison.
        In Meth. Enz., R. F. Doolittle, ed. (San Diego: Academic Press) 266:227-258',
    url: null}
homepage_links: ['http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml']
env: {}
source_links: ['http://faculty.virginia.edu/wrpearson/fasta/']