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wossname |
The program has been written on the assumption that most people will use it to quickly find the name of a program based on that program's description, so the output goes to the screen by default.
This program may find some use in automatically generating lists of EMBOSS programs and their groups for Web pages.
Search for programs with 'restrict' in their description:
% wossname restrict Finds programs by keywords in their one-line documentation SEARCH FOR 'RESTRICT' erestml Restriction site Maximum Likelihood method frestboot Bootstrapped restriction sites algorithm frestdist Distance matrix from restriction sites or fragments frestml Restriction site maximum Likelihood method recoder Remove restriction sites but maintain same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display sequence with restriction sites, translation etc restover Find restriction enzymes producing specific overhang restrict Finds restriction enzyme cleavage sites showseq Display a sequence with features, translation etc silent Silent mutation restriction enzyme scan |
Example 2
Display a listing of programs in their groups:
% wossname -search '' Finds programs by keywords in their one-line documentation ACD acdc ACD compiler acdpretty ACD pretty printing utility acdtable Creates an HTML table from an ACD file acdtrace ACD compiler on-screen trace acdvalid ACD file validation ALIGNMENT CONSENSUS cons Creates a consensus from multiple alignments megamerger Merge two large overlapping nucleic acid sequences merger Merge two overlapping sequences ALIGNMENT DIFFERENCES diffseq Find differences between nearly identical sequences ALIGNMENT DOT PLOTS dotmatcher Displays a thresholded dotplot of two sequences dotpath Non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences polydot Displays all-against-all dotplots of a set of sequences ALIGNMENT GLOBAL esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST and genomic DNA sequences needle Needleman-Wunsch global alignment stretcher Finds the best global alignment between two sequences ALIGNMENT LOCAL matcher Finds the best local alignments between two sequences seqmatchall All-against-all comparison of a set of sequences supermatcher Match large sequences against one or more other sequences water Smith-Waterman local alignment wordfinder Match large sequences against one or more other sequences wordmatch Finds all exact matches of a given size between 2 sequences ALIGNMENT MULTIPLE edialign Local multiple alignment of sequences emma Multiple alignment program - interface to ClustalW program infoalign Information on a multiple sequence alignment mse Multiple Sequence Editor plotcon Plot quality of conservation of a sequence alignment prettyplot Displays aligned sequences, with colouring and boxing showalign Displays a multiple sequence alignment tranalign Align nucleic coding regions given the aligned proteins DISPLAY abiview Reads ABI file and display the trace cirdna Draws circular maps of DNA constructs lindna Draws linear maps of DNA constructs pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices prettyplot Displays aligned sequences, with colouring and boxing prettyseq Output sequence with translated ranges remap Display sequence with restriction sites, translation etc seealso Finds programs sharing group names showalign Displays a multiple sequence alignment showdb Displays information on the currently available databases showfeat Show features of a sequence showseq Display a sequence with features, translation etc sixpack Display a DNA sequence with 6-frame translation and ORFs textsearch Search sequence documentation. Slow, use SRS and Entrez! EDIT biosed Replace or delete sequence sections codcopy Reads and writes a codon usage table cutseq Removes a specified section from a sequence degapseq Removes gap characters from sequences descseq Alter the name or description of a sequence entret Reads and writes (returns) flatfile entries extractalign Extract regions from a sequence alignment extractfeat Extract features from a sequence extractseq Extract regions from a sequence listor Write a list file of the logical OR of two sets of sequences makenucseq Creates random nucleotide sequences makeprotseq Creates random protein sequences maskfeat Mask off features of a sequence maskseq Mask off regions of a sequence newseq Type in a short new sequence noreturn Removes carriage return from ASCII files notseq Exclude a set of sequences and write out the remaining ones nthseq Writes one sequence from a multiple set of sequences pasteseq Insert one sequence into another revseq Reverse and complement a sequence seqret Reads and writes (returns) sequences seqretsplit Reads and writes (returns) sequences in individual files skipseq Reads and writes (returns) sequences, skipping first few splitter Split a sequence into (overlapping) smaller sequences trimest Trim poly-A tails off EST sequences trimseq Trim ambiguous bits off the ends of sequences union Reads sequence fragments and builds one sequence vectorstrip Strips out DNA between a pair of vector sequences yank Reads a sequence range, appends the full USA to a list file ENZYME KINETICS findkm Find Km and Vmax for an enzyme reaction FEATURE TABLES coderet Extract CDS, mRNA and translations from feature tables extractfeat Extract features from a sequence maskfeat Mask off features of a sequence showfeat Show features of a sequence twofeat Finds neighbouring pairs of features in sequences HMM ehmmalign Align sequences to an HMM profile ehmmbuild Build a profile HMM from an alignment ehmmcalibrate Calibrate HMM search statistics ehmmconvert Convert between profile HMM file formats ehmmemit Generate sequences from a profile HMM ehmmfetch Retrieve an HMM from an HMM database ehmmindex Create a binary SSI index for an HMM database ehmmpfam Search one or more sequences against an HMM database ehmmsearch Search a sequence database with a profile HMM oalistat Statistics for multiple alignment files ohmmalign Align sequences with an HMM ohmmbuild Build HMM ohmmcalibrate Calibrate a hidden Markov model ohmmconvert Convert between HMM formats ohmmemit Extract HMM sequences ohmmfetch Extract HMM from a database ohmmindex Index an HMM database ohmmpfam Align single sequence with an HMM ohmmsearch Search sequence database with an HMM INFORMATION infoalign Information on a multiple sequence alignment infoseq Displays some simple information about sequences seealso Finds programs sharing group names showdb Displays information on the currently available databases textsearch Search sequence documentation. Slow, use SRS and Entrez! tfm Displays a program's help documentation manual whichdb Search all databases for an entry wossname Finds programs by keywords in their one-line documentation MENUS emnu Simple menu of EMBOSS applications NUCLEIC 2D STRUCTURE einverted Finds DNA inverted repeats vrnaalifold RNA alignment folding vrnaalifoldpf RNA alignment folding with partition vrnacofold RNA cofolding vrnacofoldconc RNA cofolding with concentrations vrnacofoldpf RNA cofolding with partitioning vrnadistance RNA distances vrnaduplex RNA duplex calculation vrnaeval RNA eval vrnaevalpair RNA eval with cofold vrnafold Calculate secondary structures of RNAs vrnafoldpf Secondary structures of RNAs with partition vrnaheat RNA melting vrnainverse RNA sequences matching a structure vrnalfold Calculate locally stable secondary structures of RNAs vrnaplot Plot vrnafold output vrnasubopt Calculate RNA suboptimals NUCLEIC CODON USAGE cai CAI codon adaptation index chips Codon usage statistics codcmp Codon usage table comparison cusp Create a codon usage table syco Synonymous codon usage Gribskov statistic plot NUCLEIC COMPOSITION banana Bending and curvature plot in B-DNA btwisted Calculates the twisting in a B-DNA sequence chaos Create a chaos game representation plot for a sequence compseq Count composition of dimer/trimer/etc words in a sequence dan Calculates DNA RNA/DNA melting temperature freak Residue/base frequency table or plot isochore Plots isochores in large DNA sequences sirna Finds siRNA duplexes in mRNA wordcount Counts words of a specified size in a DNA sequence NUCLEIC CPG ISLANDS cpgplot Plot CpG rich areas cpgreport Reports all CpG rich regions geecee Calculates fractional GC content of nucleic acid sequences newcpgreport Report CpG rich areas newcpgseek Reports CpG rich regions NUCLEIC GENE FINDING getorf Finds and extracts open reading frames (ORFs) marscan Finds MAR/SAR sites in nucleic sequences plotorf Plot potential open reading frames showorf Pretty output of DNA translations sixpack Display a DNA sequence with 6-frame translation and ORFs syco Synonymous codon usage Gribskov statistic plot tcode Fickett TESTCODE statistic to identify protein-coding DNA wobble Wobble base plot NUCLEIC MOTIFS dreg Regular expression search of a nucleotide sequence fuzznuc Nucleic acid pattern search fuzztran Protein pattern search after translation marscan Finds MAR/SAR sites in nucleic sequences NUCLEIC MUTATION msbar Mutate sequence beyond all recognition shuffleseq Shuffles a set of sequences maintaining composition NUCLEIC PRIMERS eprimer3 Picks PCR primers and hybridization oligos primersearch Searches DNA sequences for matches with primer pairs stssearch Search a DNA database for matches with a set of STS primers NUCLEIC PROFILES profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles NUCLEIC REPEATS einverted Finds DNA inverted repeats equicktandem Finds tandem repeats etandem Looks for tandem repeats in a nucleotide sequence palindrome Looks for inverted repeats in a nucleotide sequence NUCLEIC RESTRICTION recoder Remove restriction sites but maintain same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display sequence with restriction sites, translation etc restover Find restriction enzymes producing specific overhang restrict Finds restriction enzyme cleavage sites showseq Display a sequence with features, translation etc silent Silent mutation restriction enzyme scan NUCLEIC RNA FOLDING vrnaalifold RNA alignment folding vrnaalifoldpf RNA alignment folding with partition vrnacofold RNA cofolding vrnacofoldconc RNA cofolding with concentrations vrnacofoldpf RNA cofolding with partitioning vrnadistance RNA distances vrnaduplex RNA duplex calculation vrnaeval RNA eval vrnaevalpair RNA eval with cofold vrnafold Calculate secondary structures of RNAs vrnafoldpf Secondary structures of RNAs with partition vrnaheat RNA melting vrnainverse RNA sequences matching a structure vrnalfold Calculate locally stable secondary structures of RNAs vrnaplot Plot vrnafold output vrnasubopt Calculate RNA suboptimals NUCLEIC TRANSCRIPTION tfscan Scans DNA sequences for transcription factors NUCLEIC TRANSLATION backtranambig Back translate a protein sequence to ambiguous codons backtranseq Back translate a protein sequence coderet Extract CDS, mRNA and translations from feature tables plotorf Plot potential open reading frames prettyseq Output sequence with translated ranges remap Display sequence with restriction sites, translation etc showorf Pretty output of DNA translations showseq Display a sequence with features, translation etc sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences PHYLOGENY CONSENSUS econsense Majority-rule and strict consensus tree fconsense Majority-rule and strict consensus tree ftreedist Distances between trees ftreedistpair Distances between two sets of trees PHYLOGENY CONTINUOUS CHARACTERS econtml Continuous character Maximum Likelihood method econtrast Continuous character Contrasts fcontrast Continuous character Contrasts PHYLOGENY DISCRETE CHARACTERS eclique Largest clique program edollop Dollo and polymorphism parsimony algorithm edolpenny Penny algorithm Dollo or polymorphism efactor Multistate to binary recoding program emix Mixed parsimony algorithm epenny Penny algorithm, branch-and-bound fclique Largest clique program fdollop Dollo and polymorphism parsimony algorithm fdolpenny Penny algorithm Dollo or polymorphism ffactor Multistate to binary recoding program fmix Mixed parsimony algorithm fmove Interactive mixed method parsimony fpars Discrete character parsimony fpenny Penny algorithm, branch-and-bound PHYLOGENY DISTANCE MATRIX efitch Fitch-Margoliash and Least-Squares Distance Methods ekitsch Fitch-Margoliash method with contemporary tips eneighbor Phylogenies from distance matrix by N-J or UPGMA method ffitch Fitch-Margoliash and Least-Squares Distance Methods fkitsch Fitch-Margoliash method with contemporary tips fneighbor Phylogenies from distance matrix by N-J or UPGMA method PHYLOGENY GENE FREQUENCIES egendist Genetic Distance Matrix program fcontml Gene frequency and continuous character Maximum Likelihood fgendist Compute genetic distances from gene frequencies PHYLOGENY MOLECULAR SEQUENCE distmat Creates a distance matrix from multiple alignments ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence Distance Matrix program ednainvar Nucleic acid sequence Invariants method ednaml Phylogenies from nucleic acid Maximum Likelihood ednamlk Phylogenies from nucleic acid Maximum Likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm erestml Restriction site Maximum Likelihood method eseqboot Bootstrapped sequences algorithm fdiscboot Bootstrapped discrete sites algorithm fdnacomp DNA compatibility algorithm fdnadist Nucleic acid sequence Distance Matrix program fdnainvar Nucleic acid sequence Invariants method fdnaml Estimates nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnamove Interactive DNA parsimony fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA fdolmove Interactive Dollo or Polymorphism Parsimony ffreqboot Bootstrapped genetic frequencies algorithm fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm fprotpars Protein parsimony algorithm frestboot Bootstrapped restriction sites algorithm frestdist Distance matrix from restriction sites or fragments frestml Restriction site maximum Likelihood method fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm PHYLOGENY TREE DRAWING fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram fdrawtree Plots an unrooted tree diagram fretree Interactive tree rearrangement PROTEIN 2D STRUCTURE garnier Predicts protein secondary structure helixturnhelix Report nucleic acid binding motifs hmoment Hydrophobic moment calculation pepcoil Predicts coiled coil regions pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices tmap Displays membrane spanning regions topo Draws an image of a transmembrane protein PROTEIN 3D STRUCTURE contacts Generate intra-chain CON files from CCF files domainalign Generate alignments (DAF file) for nodes in a DCF file domainrep Reorder DCF file to identify representative structures domainreso Remove low resolution domains from a DCF file interface Generate inter-chain CON files from CCF files libgen Generate discriminating elements from alignments matgen3d Generate a 3D-1D scoring matrix from CCF files psiphi Phi and psi torsion angles from protein coordinates rocon Generates a hits file from comparing two DHF files rocplot Performs ROC analysis on hits files seqalign Extend alignments (DAF file) with sequences (DHF file) seqfraggle Removes fragment sequences from DHF files seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file seqsort Remove ambiguous classified sequences from DHF files seqwords Generates DHF files from keyword search of UniProt siggen Generates a sparse protein signature from an alignment siggenlig Generate ligand-binding signatures from a CON file sigscan Generate hits (DHF file) from a signature search sigscanlig Search ligand-signature library & write hits (LHF file) PROTEIN COMPOSITION backtranambig Back translate a protein sequence to ambiguous codons backtranseq Back translate a protein sequence charge Protein charge plot checktrans Reports STOP codons and ORF statistics of a protein compseq Count composition of dimer/trimer/etc words in a sequence emowse Protein identification by mass spectrometry freak Residue/base frequency table or plot iep Calculates the isoelectric point of a protein mwcontam Shows molwts that match across a set of files mwfilter Filter noisy molwts from mass spec output octanol Displays protein hydropathy pepinfo Plots simple amino acid properties in parallel pepstats Protein statistics pepwindow Displays protein hydropathy pepwindowall Displays protein hydropathy of a set of sequences PROTEIN MOTIFS antigenic Finds antigenic sites in proteins digest Protein proteolytic enzyme or reagent cleavage digest emast Motif detection ememe Motif detection epestfind Finds PEST motifs as potential proteolytic cleavage sites fuzzpro Protein pattern search fuzztran Protein pattern search after translation helixturnhelix Report nucleic acid binding motifs oddcomp Find protein sequence regions with a biased composition omeme Motif detection patmatdb Search a protein sequence with a motif patmatmotifs Search a PROSITE motif database with a protein sequence pepcoil Predicts coiled coil regions preg Regular expression search of a protein sequence pscan Scans proteins using PRINTS sigcleave Reports protein signal cleavage sites PROTEIN MUTATION msbar Mutate sequence beyond all recognition shuffleseq Shuffles a set of sequences maintaining composition PROTEIN PROFILES profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles TEST crystalball Answers every drug discovery question about a sequence myseq Demonstration of sequence reading mytest Demonstration of sequence reading UTILS DATABASE CREATION aaindexextract Extract data from AAINDEX allversusall Sequence similarity data from all-versus-all comparison cathparse Generates DCF file from raw CATH files cutgextract Extract data from CUTG domainer Generates domain CCF files from protein CCF files domainnr Removes redundant domains from a DCF file domainseqs Adds sequence records to a DCF file domainsse Add secondary structure records to a DCF file hetparse Converts heterogen group dictionary to EMBL-like format pdbparse Parses PDB files and writes protein CCF files pdbplus Add accessibility & secondary structure to a CCF file pdbtosp Convert swissprot:PDB codes file to EMBL-like format printsextract Extract data from PRINTS prosextract Build the PROSITE motif database for use by patmatmotifs rebaseextract Extract data from REBASE scopparse Generate DCF file from raw SCOP files seqnr Removes redundancy from DHF files sites Generate residue-ligand CON files from CCF files ssematch Search a DCF file for secondary structure matches tfextract Extract data from TRANSFAC UTILS DATABASE INDEXING dbiblast Index a BLAST database dbifasta Database indexing for fasta file databases dbiflat Index a flat file database dbigcg Index a GCG formatted database dbxfasta Database b+tree indexing for fasta file databases dbxflat Database b+tree indexing for flat file databases dbxgcg Database b+tree indexing for GCG formatted databases UTILS MISC embossdata Finds or fetches data files read by EMBOSS programs embossversion Writes the current EMBOSS version number |
Example 3
Display an alphabetic listing of all programs:
% wossname -search '' -alphabetic Finds programs by keywords in their one-line documentation ALPHABETIC LIST OF PROGRAMS aaindexextract Extract data from AAINDEX abiview Reads ABI file and display the trace acdc ACD compiler acdpretty ACD pretty printing utility acdtable Creates an HTML table from an ACD file acdtrace ACD compiler on-screen trace acdvalid ACD file validation allversusall Sequence similarity data from all-versus-all comparison antigenic Finds antigenic sites in proteins backtranambig Back translate a protein sequence to ambiguous codons backtranseq Back translate a protein sequence banana Bending and curvature plot in B-DNA biosed Replace or delete sequence sections btwisted Calculates the twisting in a B-DNA sequence cai CAI codon adaptation index cathparse Generates DCF file from raw CATH files chaos Create a chaos game representation plot for a sequence charge Protein charge plot checktrans Reports STOP codons and ORF statistics of a protein chips Codon usage statistics cirdna Draws circular maps of DNA constructs codcmp Codon usage table comparison codcopy Reads and writes a codon usage table coderet Extract CDS, mRNA and translations from feature tables compseq Count composition of dimer/trimer/etc words in a sequence cons Creates a consensus from multiple alignments contacts Generate intra-chain CON files from CCF files cpgplot Plot CpG rich areas cpgreport Reports all CpG rich regions crystalball Answers every drug discovery question about a sequence cusp Create a codon usage table cutgextract Extract data from CUTG cutseq Removes a specified section from a sequence dan Calculates DNA RNA/DNA melting temperature dbiblast Index a BLAST database dbifasta Database indexing for fasta file databases dbiflat Index a flat file database dbigcg Index a GCG formatted database dbxfasta Database b+tree indexing for fasta file databases dbxflat Database b+tree indexing for flat file databases dbxgcg Database b+tree indexing for GCG formatted databases degapseq Removes gap characters from sequences descseq Alter the name or description of a sequence diffseq Find differences between nearly identical sequences digest Protein proteolytic enzyme or reagent cleavage digest distmat Creates a distance matrix from multiple alignments domainalign Generate alignments (DAF file) for nodes in a DCF file domainer Generates domain CCF files from protein CCF files domainnr Removes redundant domains from a DCF file domainrep Reorder DCF file to identify representative structures domainreso Remove low resolution domains from a DCF file domainseqs Adds sequence records to a DCF file domainsse Add secondary structure records to a DCF file dotmatcher Displays a thresholded dotplot of two sequences dotpath Non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences dreg Regular expression search of a nucleotide sequence eclique Largest clique program econsense Majority-rule and strict consensus tree econtml Continuous character Maximum Likelihood method econtrast Continuous character Contrasts edialign Local multiple alignment of sequences ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence Distance Matrix program ednainvar Nucleic acid sequence Invariants method ednaml Phylogenies from nucleic acid Maximum Likelihood ednamlk Phylogenies from nucleic acid Maximum Likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA edollop Dollo and polymorphism parsimony algorithm edolpenny Penny algorithm Dollo or polymorphism efactor Multistate to binary recoding program efitch Fitch-Margoliash and Least-Squares Distance Methods egendist Genetic Distance Matrix program ehmmalign Align sequences to an HMM profile ehmmbuild Build a profile HMM from an alignment ehmmcalibrate Calibrate HMM search statistics ehmmconvert Convert between profile HMM file formats ehmmemit Generate sequences from a profile HMM ehmmfetch Retrieve an HMM from an HMM database ehmmindex Create a binary SSI index for an HMM database ehmmpfam Search one or more sequences against an HMM database ehmmsearch Search a sequence database with a profile HMM einverted Finds DNA inverted repeats ekitsch Fitch-Margoliash method with contemporary tips emast Motif detection embossdata Finds or fetches data files read by EMBOSS programs embossversion Writes the current EMBOSS version number ememe Motif detection emix Mixed parsimony algorithm emma Multiple alignment program - interface to ClustalW program emnu Simple menu of EMBOSS applications emowse Protein identification by mass spectrometry eneighbor Phylogenies from distance matrix by N-J or UPGMA method entret Reads and writes (returns) flatfile entries epenny Penny algorithm, branch-and-bound epestfind Finds PEST motifs as potential proteolytic cleavage sites eprimer3 Picks PCR primers and hybridization oligos eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm equicktandem Finds tandem repeats erestml Restriction site Maximum Likelihood method eseqboot Bootstrapped sequences algorithm esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST and genomic DNA sequences etandem Looks for tandem repeats in a nucleotide sequence extractalign Extract regions from a sequence alignment extractfeat Extract features from a sequence extractseq Extract regions from a sequence fclique Largest clique program fconsense Majority-rule and strict consensus tree fcontml Gene frequency and continuous character Maximum Likelihood fcontrast Continuous character Contrasts fdiscboot Bootstrapped discrete sites algorithm fdnacomp DNA compatibility algorithm fdnadist Nucleic acid sequence Distance Matrix program fdnainvar Nucleic acid sequence Invariants method fdnaml Estimates nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnamove Interactive DNA parsimony fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA fdollop Dollo and polymorphism parsimony algorithm fdolmove Interactive Dollo or Polymorphism Parsimony fdolpenny Penny algorithm Dollo or polymorphism fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram fdrawtree Plots an unrooted tree diagram ffactor Multistate to binary recoding program ffitch Fitch-Margoliash and Least-Squares Distance Methods ffreqboot Bootstrapped genetic frequencies algorithm fgendist Compute genetic distances from gene frequencies findkm Find Km and Vmax for an enzyme reaction fkitsch Fitch-Margoliash method with contemporary tips fmix Mixed parsimony algorithm fmove Interactive mixed method parsimony fneighbor Phylogenies from distance matrix by N-J or UPGMA method fpars Discrete character parsimony fpenny Penny algorithm, branch-and-bound fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm fprotpars Protein parsimony algorithm freak Residue/base frequency table or plot frestboot Bootstrapped restriction sites algorithm frestdist Distance matrix from restriction sites or fragments frestml Restriction site maximum Likelihood method fretree Interactive tree rearrangement fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm ftreedist Distances between trees ftreedistpair Distances between two sets of trees fuzznuc Nucleic acid pattern search fuzzpro Protein pattern search fuzztran Protein pattern search after translation garnier Predicts protein secondary structure geecee Calculates fractional GC content of nucleic acid sequences getorf Finds and extracts open reading frames (ORFs) helixturnhelix Report nucleic acid binding motifs hetparse Converts heterogen group dictionary to EMBL-like format hmoment Hydrophobic moment calculation iep Calculates the isoelectric point of a protein infoalign Information on a multiple sequence alignment infoseq Displays some simple information about sequences interface Generate inter-chain CON files from CCF files isochore Plots isochores in large DNA sequences libgen Generate discriminating elements from alignments lindna Draws linear maps of DNA constructs listor Write a list file of the logical OR of two sets of sequences makenucseq Creates random nucleotide sequences makeprotseq Creates random protein sequences marscan Finds MAR/SAR sites in nucleic sequences maskfeat Mask off features of a sequence maskseq Mask off regions of a sequence matcher Finds the best local alignments between two sequences matgen3d Generate a 3D-1D scoring matrix from CCF files megamerger Merge two large overlapping nucleic acid sequences merger Merge two overlapping sequences msbar Mutate sequence beyond all recognition mse Multiple Sequence Editor mwcontam Shows molwts that match across a set of files mwfilter Filter noisy molwts from mass spec output myseq Demonstration of sequence reading mytest Demonstration of sequence reading needle Needleman-Wunsch global alignment newcpgreport Report CpG rich areas newcpgseek Reports CpG rich regions newseq Type in a short new sequence noreturn Removes carriage return from ASCII files notseq Exclude a set of sequences and write out the remaining ones nthseq Writes one sequence from a multiple set of sequences oalistat Statistics for multiple alignment files octanol Displays protein hydropathy oddcomp Find protein sequence regions with a biased composition ohmmalign Align sequences with an HMM ohmmbuild Build HMM ohmmcalibrate Calibrate a hidden Markov model ohmmconvert Convert between HMM formats ohmmemit Extract HMM sequences ohmmfetch Extract HMM from a database ohmmindex Index an HMM database ohmmpfam Align single sequence with an HMM ohmmsearch Search sequence database with an HMM omeme Motif detection palindrome Looks for inverted repeats in a nucleotide sequence pasteseq Insert one sequence into another patmatdb Search a protein sequence with a motif patmatmotifs Search a PROSITE motif database with a protein sequence pdbparse Parses PDB files and writes protein CCF files pdbplus Add accessibility & secondary structure to a CCF file pdbtosp Convert swissprot:PDB codes file to EMBL-like format pepcoil Predicts coiled coil regions pepinfo Plots simple amino acid properties in parallel pepnet Displays proteins as a helical net pepstats Protein statistics pepwheel Shows protein sequences as helices pepwindow Displays protein hydropathy pepwindowall Displays protein hydropathy of a set of sequences plotcon Plot quality of conservation of a sequence alignment plotorf Plot potential open reading frames polydot Displays all-against-all dotplots of a set of sequences preg Regular expression search of a protein sequence prettyplot Displays aligned sequences, with colouring and boxing prettyseq Output sequence with translated ranges primersearch Searches DNA sequences for matches with primer pairs printsextract Extract data from PRINTS profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles prosextract Build the PROSITE motif database for use by patmatmotifs pscan Scans proteins using PRINTS psiphi Phi and psi torsion angles from protein coordinates rebaseextract Extract data from REBASE recoder Remove restriction sites but maintain same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display sequence with restriction sites, translation etc restover Find restriction enzymes producing specific overhang restrict Finds restriction enzyme cleavage sites revseq Reverse and complement a sequence rocon Generates a hits file from comparing two DHF files rocplot Performs ROC analysis on hits files scopparse Generate DCF file from raw SCOP files seealso Finds programs sharing group names seqalign Extend alignments (DAF file) with sequences (DHF file) seqfraggle Removes fragment sequences from DHF files seqmatchall All-against-all comparison of a set of sequences seqnr Removes redundancy from DHF files seqret Reads and writes (returns) sequences seqretsplit Reads and writes (returns) sequences in individual files seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file seqsort Remove ambiguous classified sequences from DHF files seqwords Generates DHF files from keyword search of UniProt showalign Displays a multiple sequence alignment showdb Displays information on the currently available databases showfeat Show features of a sequence showorf Pretty output of DNA translations showseq Display a sequence with features, translation etc shuffleseq Shuffles a set of sequences maintaining composition sigcleave Reports protein signal cleavage sites siggen Generates a sparse protein signature from an alignment siggenlig Generate ligand-binding signatures from a CON file sigscan Generate hits (DHF file) from a signature search sigscanlig Search ligand-signature library & write hits (LHF file) silent Silent mutation restriction enzyme scan sirna Finds siRNA duplexes in mRNA sites Generate residue-ligand CON files from CCF files sixpack Display a DNA sequence with 6-frame translation and ORFs skipseq Reads and writes (returns) sequences, skipping first few splitter Split a sequence into (overlapping) smaller sequences ssematch Search a DCF file for secondary structure matches stretcher Finds the best global alignment between two sequences stssearch Search a DNA database for matches with a set of STS primers supermatcher Match large sequences against one or more other sequences syco Synonymous codon usage Gribskov statistic plot tcode Fickett TESTCODE statistic to identify protein-coding DNA textsearch Search sequence documentation. Slow, use SRS and Entrez! tfextract Extract data from TRANSFAC tfm Displays a program's help documentation manual tfscan Scans DNA sequences for transcription factors tmap Displays membrane spanning regions topo Draws an image of a transmembrane protein tranalign Align nucleic coding regions given the aligned proteins transeq Translate nucleic acid sequences trimest Trim poly-A tails off EST sequences trimseq Trim ambiguous bits off the ends of sequences twofeat Finds neighbouring pairs of features in sequences union Reads sequence fragments and builds one sequence vectorstrip Strips out DNA between a pair of vector sequences vrnaalifold RNA alignment folding vrnaalifoldpf RNA alignment folding with partition vrnacofold RNA cofolding vrnacofoldconc RNA cofolding with concentrations vrnacofoldpf RNA cofolding with partitioning vrnadistance RNA distances vrnaduplex RNA duplex calculation vrnaeval RNA eval vrnaevalpair RNA eval with cofold vrnafold Calculate secondary structures of RNAs vrnafoldpf Secondary structures of RNAs with partition vrnaheat RNA melting vrnainverse RNA sequences matching a structure vrnalfold Calculate locally stable secondary structures of RNAs vrnaplot Plot vrnafold output vrnasubopt Calculate RNA suboptimals water Smith-Waterman local alignment whichdb Search all databases for an entry wobble Wobble base plot wordcount Counts words of a specified size in a DNA sequence wordfinder Match large sequences against one or more other sequences wordmatch Finds all exact matches of a given size between 2 sequences wossname Finds programs by keywords in their one-line documentation yank Reads a sequence range, appends the full USA to a list file |
Example 4
Display only the groups that the programs can belong to:
% wossname -search '' -groups Finds programs by keywords in their one-line documentation ACD ALIGNMENT CONSENSUS ALIGNMENT DIFFERENCES ALIGNMENT DOT PLOTS ALIGNMENT GLOBAL ALIGNMENT LOCAL ALIGNMENT MULTIPLE DISPLAY EDIT ENZYME KINETICS FEATURE TABLES HMM INFORMATION MENUS NUCLEIC 2D STRUCTURE NUCLEIC CODON USAGE NUCLEIC COMPOSITION NUCLEIC CPG ISLANDS NUCLEIC GENE FINDING NUCLEIC MOTIFS NUCLEIC MUTATION NUCLEIC PRIMERS NUCLEIC PROFILES NUCLEIC REPEATS NUCLEIC RESTRICTION NUCLEIC RNA FOLDING NUCLEIC TRANSCRIPTION NUCLEIC TRANSLATION PHYLOGENY CONSENSUS PHYLOGENY CONTINUOUS CHARACTERS PHYLOGENY DISCRETE CHARACTERS PHYLOGENY DISTANCE MATRIX PHYLOGENY GENE FREQUENCIES PHYLOGENY MOLECULAR SEQUENCE PHYLOGENY TREE DRAWING PROTEIN 2D STRUCTURE PROTEIN 3D STRUCTURE PROTEIN COMPOSITION PROTEIN MOTIFS PROTEIN MUTATION PROTEIN PROFILES TEST UTILS DATABASE CREATION UTILS DATABASE INDEXING UTILS MISC |
Example 5
Output html tags around the list of programs:
% wossname '' -html -out wossname.html Finds programs by keywords in their one-line documentation |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-search] string Enter a word or words here and a
case-independent search for it will be made
in the one-line documentation, group names
and keywords of all of the EMBOSS programs.
If no keyword is specified, all programs
will be listed. (Any string is accepted)
Additional (Optional) qualifiers:
-explode boolean [N] The groups that EMBOSS applications
belong to have two forms, exploded and not
exploded. The exploded group names are more
numerous and often vaguely phrased than the
non-exploded ones. The exploded names are
formed from definitions of the group names
that start like NAME1:NAME2 and which are
then expanded into many combinations of the
names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
NAME2 NAME1'. The non-expanded names are
simply like: 'NAME1 NAME2'.
-[no]allmatch boolean [Y] By default, all words in the search
string must match. This option searches for
a match to any word in a list of
possibilities
-showkeywords boolean [N] Show keywords with program documentation
-outfile outfile [stdout] Output file name
-html toggle [N] If you are sending the output to a file,
this will format it for displaying as a
table in a WWW document.
-groups boolean [N] If you use this option, then only the
group names will output to the file
-alphabetic boolean [N] If you use this option, then you will
get a single list of the program names and
descriptions instead of the programs being
listed in their functional groups.
Advanced (Unprompted) qualifiers:
-[no]emboss boolean [Y] If you use this option then EMBOSS
program documentation will be searched. If
this option is set to be false, then only
the EMBASSY programs will be searched (if
the -embassy option is true). EMBASSY
programs are not strictly part of EMBOSS,
but use the same code libraries and share
the same look and feel, but are generally
developed by people who wish the programs to
be outside of the GNU Public Licence scheme
-[no]embassy boolean [Y] If you use this option then EMBASSY
program documentation will be searched. If
this option is set to be false, then only
the EMBOSS programs will be searched (if the
-emboss option is true). EMBASSY programs
are not strictly part of EMBOSS, but use the
same code libraries and share the same look
and feel, but are generally developed by
people who wish the programs to be outside
of the GNU Public Licence scheme
-showembassy string If you use this option then this EMBASSY
package program documentation will be
searched. EMBASSY programs are not strictly
part of EMBOSS, but use the same code
libraries and share the same look and feel,
but are generally developed by people who
wish the programs to be outside of the GNU
Public Licence scheme (Any string is
accepted)
-colon boolean [N] The groups that EMBOSS applications
belong to up to two levels, for example the
primary group 'ALIGNMENT' has several
sub-groups, or second-level groups, e.g.:
CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
LOCAL, MULTIPLE. To aid programs that parse
the output of wossname that require the
names of these subgroups, a colon ':' will
be placed between the first and second level
of the group name if this option is true.
Note: This does not apply if the group names
have been exploded with the 'explode'
option.
-gui boolean [N] This option is intended to help those
who are designing Graphical User Interfaces
to the EMBOSS applications. Some EMBOSS
programs are inappropriate for running in a
GUI, these include other menu programs and
interactive editors. This option allows you
to only report those programs that can be
run from a GUI
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-search] (Parameter 1) |
Enter a word or words here and a case-independent search for it will be made in the one-line documentation, group names and keywords of all of the EMBOSS programs. If no keyword is specified, all programs will be listed. | Any string is accepted | An empty string is accepted |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -explode | The groups that EMBOSS applications belong to have two forms, exploded and not exploded. The exploded group names are more numerous and often vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The non-expanded names are simply like: 'NAME1 NAME2'. | Boolean value Yes/No | No |
| -[no]allmatch | By default, all words in the search string must match. This option searches for a match to any word in a list of possibilities | Boolean value Yes/No | Yes |
| -showkeywords | Show keywords with program documentation | Boolean value Yes/No | No |
| -outfile | Output file name | Output file | stdout |
| -html | If you are sending the output to a file, this will format it for displaying as a table in a WWW document. | Toggle value Yes/No | No |
| -groups | If you use this option, then only the group names will output to the file | Boolean value Yes/No | No |
| -alphabetic | If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups. | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]emboss | If you use this option then EMBOSS program documentation will be searched. If this option is set to be false, then only the EMBASSY programs will be searched (if the -embassy option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme | Boolean value Yes/No | Yes |
| -[no]embassy | If you use this option then EMBASSY program documentation will be searched. If this option is set to be false, then only the EMBOSS programs will be searched (if the -emboss option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme | Boolean value Yes/No | Yes |
| -showembassy | If you use this option then this EMBASSY package program documentation will be searched. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme | Any string is accepted | An empty string is accepted |
| -colon | The groups that EMBOSS applications belong to up to two levels, for example the primary group 'ALIGNMENT' has several sub-groups, or second-level groups, e.g.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE. To aid programs that parse the output of wossname that require the names of these subgroups, a colon ':' will be placed between the first and second level of the group name if this option is true. Note: This does not apply if the group names have been exploded with the 'explode' option. | Boolean value Yes/No | No |
| -gui | This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors. This option allows you to only report those programs that can be run from a GUI | Boolean value Yes/No | No |
wossname reads the brief descriptions and the program groups from the ACD files. (ACD files control the parameters that the programs expect - don't worry about them unless you are writing EMBOSS programs).
The format of ACD files is documented elsewhere.
| <h2><a name="ACD">ACD</a></h2> <table border cellpadding=4 bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr> <tr> <td><a href="acdc.html">acdc</a></td> <td>ACD compiler</td> </tr> <tr> <td><a href="acdpretty.html">acdpretty</a></td> <td>ACD pretty printing utility</td> </tr> <tr> <td><a href="acdtable.html">acdtable</a></td> <td>Creates an HTML table from an ACD file</td> </tr> <tr> <td><a href="acdtrace.html">acdtrace</a></td> <td>ACD compiler on-screen trace</td> </tr> <tr> <td><a href="acdvalid.html">acdvalid</a></td> <td>ACD file validation</td> </tr> </table> <h2><a name="ALIGNMENT CONSENSUS">ALIGNMENT CONSENSUS</a></h2> <table border cellpadding=4 bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr> <tr> <td><a href="cons.html">cons</a></td> <td>Creates a consensus from multiple alignments</td> </tr> <tr> <td><a href="megamerger.html">megamerger</a></td> <td>Merge two large overlapping nucleic acid sequences</td> </tr> <tr> <td><a href="merger.html">merger</a></td> <td>Merge two overlapping sequences</td> </tr> </table> <h2><a name="ALIGNMENT DIFFERENCES">ALIGNMENT DIFFERENCES</a></h2> <table border cellpadding=4 bgcolor="#FFFFF0"> [Part of this file has been deleted for brevity] <tr><th>Program name</th><th>Description</th></tr> <tr> <td><a href="dbiblast.html">dbiblast</a></td> <td>Index a BLAST database</td> </tr> <tr> <td><a href="dbifasta.html">dbifasta</a></td> <td>Database indexing for fasta file databases</td> </tr> <tr> <td><a href="dbiflat.html">dbiflat</a></td> <td>Index a flat file database</td> </tr> <tr> <td><a href="dbigcg.html">dbigcg</a></td> <td>Index a GCG formatted database</td> </tr> <tr> <td><a href="dbxfasta.html">dbxfasta</a></td> <td>Database b+tree indexing for fasta file databases</td> </tr> <tr> <td><a href="dbxflat.html">dbxflat</a></td> <td>Database b+tree indexing for flat file databases</td> </tr> <tr> <td><a href="dbxgcg.html">dbxgcg</a></td> <td>Database b+tree indexing for GCG formatted databases</td> </tr> </table> <h2><a name="UTILS MISC">UTILS MISC</a></h2> <table border cellpadding=4 bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr> <tr> <td><a href="embossdata.html">embossdata</a></td> <td>Finds or fetches data files read by EMBOSS programs</td> </tr> <tr> <td><a href="embossversion.html">embossversion</a></td> <td>Writes the current EMBOSS version number</td> </tr> </table> |
If the -html, -prelink and -postlink qualifiers are specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the list of programs is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.
A program can belong to more than one group.
The name of this program comes from its use as a favorite word of the author Terry Pratchett. It is used especially by the characters of the parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.
| Program name | Description |
|---|---|
| infoalign | Information on a multiple sequence alignment |
| infoseq | Displays some simple information about sequences |
| seealso | Finds programs sharing group names |
| showdb | Displays information on the currently available databases |
| textsearch | Search sequence documentation. Slow, use SRS and Entrez! |
| tfm | Displays a program's help documentation manual |
| whichdb | Search all databases for an entry |