wossname Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Find programs by keywords in their short description Description wossname searches for the specified keywords (or parts thereof) in the application short description (as displayed by a program when it starts), functional group name and keywords. The group name, application name and short description of any matching applications is output (screen by default). If no search words are specified, then details of all the EMBOSS programs are output. There are various options for controlling how the search is performed and what is given in the output file. Optionally, the output will be wrapped in HTML tags ready for inclusion in a Web page. Usage Here is a sample session with wossname Search for programs with 'restrict' in their description: % wossname restrict Find programs by keywords in their short description SEARCH FOR 'RESTRICT' erestml Restriction site maximum likelihood method frestboot Bootstrapped restriction sites algorithm frestdist Calculate distance matrix from restriction sites or fragments frestml Restriction site maximum likelihood method rebaseextract Process the REBASE database for use by restriction enzyme applicat ions recoder Find restriction sites to remove (mutate) with no translation chan ge redata Retrieve information from REBASE restriction enzyme database remap Display restriction enzyme binding sites in a nucleotide sequence restover Find restriction enzymes producing a specific overhang restrict Report restriction enzyme cleavage sites in a nucleotide sequence showseq Display sequences with features in pretty format silent Find restriction sites to insert (mutate) with no translation chan ge Example 2 Display a listing of programs in their groups: % wossname -search "" Find programs by keywords in their short description ACD acdc Test an application ACD file acdpretty Correctly reformat an application ACD file acdtable Generate an HTML table of parameters from an application ACD file acdtrace Trace processing of an application ACD file (for testing) acdvalid Validate an application ACD file ALIGNMENT extractalign Extract regions from a sequence alignment ALIGNMENT CONSENSUS cons Create a consensus sequence from a multiple alignment consambig Create an ambiguous consensus sequence from a multiple alignment megamerger Merge two large overlapping DNA sequences merger Merge two overlapping sequences ALIGNMENT DIFFERENCES diffseq Compare and report features of two similar sequences ALIGNMENT DOT PLOTS dotmatcher Draw a threshold dotplot of two sequences dotpath Draw a non-overlapping wordmatch dotplot of two sequences dottup Display a wordmatch dotplot of two sequences polydot Draw dotplots for all-against-all comparison of a sequence set ALIGNMENT GLOBAL esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST sequences to genomic DNA sequence needle Needleman-Wunsch global alignment of two sequences needleall Many-to-many pairwise alignments of two sequence sets stretcher Needleman-Wunsch rapid global alignment of two sequences ALIGNMENT LOCAL domainalign Generate alignments (DAF file) for nodes in a DCF file domainrep Reorder DCF file to identify representative structures matcher Waterman-Eggert local alignment of two sequences oalistat Statistics for multiple alignment files seqalign Extend alignments (DAF file) with sequences (DHF file) seqmatchall All-against-all word comparison of a sequence set supermatcher Calculate approximate local pair-wise alignments of larger sequence s water Smith-Waterman local alignment of sequences wordfinder Match large sequences against one or more other sequences wordmatch Find regions of identity (exact matches) of two sequences ALIGNMENT MULTIPLE edialign Local multiple alignment of sequences emma Multiple sequence alignment (ClustalW wrapper) eomega Multiple sequence alignment (ClustalO wrapper) eomegapp Profile with profile (ClustalO wrapper) eomegaps Single sequence with profile (ClustalO wrapper) eomegash Sequence with HMM (ClustalO wrapper) eomegasp Sequence with profile (ClustalO wrapper) infoalign Display basic information about a multiple sequence alignment mse Multiple sequence editor plotcon Plot conservation of a sequence alignment prettyplot Draw a sequence alignment with pretty formatting showalign Display a multiple sequence alignment in pretty format tranalign Generate an alignment of nucleic coding regions from aligned proteins ASSEMBLY FRAGMENT ASSEMBLY emira MIRA fragment assembly program emiraest MIRAest fragment assembly program DATA RESOURCES cachedas Generate server cache file for DAS servers or for the DAS regis try cachedbfetch Generate server cache file for Dbfetch/WSDbfetch data sources cacheebeyesearch Generate server cache file for EB-eye search domains cacheensembl Generate server cache file for an Ensembl server dbtell Display information about a public database servertell Display information about a public server showdb Display information on configured databases showserver Display information on configured servers DATA RETRIEVAL codcopy Copy and reformat a codon usage table seqret Read and write (return) sequences DATA RETRIEVAL CHEMISTRY DATA infobase Return information on a given nucleotide base inforesidue Return information on a given amino acid residue DATA RETRIEVAL FEATURE DATA featcopy Read and write a feature table featmerge Merge two overlapping feature tables DATA RETRIEVAL ONTOLOGY DATA edamdef Find EDAM ontology terms by definition edamhasinput Find EDAM ontology terms by has_input relation edamhasoutput Find EDAM ontology terms by has_output relation edamisformat Find EDAM ontology terms by is_format_of relation edamisid Find EDAM ontology terms by is_identifier_of relation edamname Find EDAM ontology terms by name godef Find GO ontology terms by definition goname Find GO ontology terms by name ontoget Get ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id ontogetobsolete Get ontology ontology terms ontogetroot Get ontology root terms by child identifier ontogetsibs Get ontology term(s) by id with common parent ontogetup Get ontology term(s) by id of child ontoisobsolete Report whether an ontology term id is obsolete ontotext Get ontology term(s) original full text DATA RETRIEVAL RESOURCE DATA drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource drget Get data resource entries drtext Get data resource entries complete text DATA RETRIEVAL SEQUENCE DATA abiview Display the trace in an ABI sequencer file coderet Extract CDS, mRNA and translations from feature tables entret Retrieve sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment infoalign Display basic information about a multiple sequence alignment infoseq Display basic information about sequences refseqget Get reference sequence seqxref Retrieve all database cross-references for a sequence entry seqxrefget Retrieve all cross-referenced data for a sequence entry showalign Display a multiple sequence alignment in pretty format variationget Get sequence variations whichdb Search all sequence databases for an entry and retrieve it DATA RETRIEVAL SEQUENCE DATA ASSEMBLY DATA assemblyget Get assembly of sequence reads infoassembly Display information about assemblies DATA RETRIEVAL TEXT DATA drtext Get data resource entries complete text entret Retrieve sequence entries from flatfile databases and files ontotext Get ontology term(s) original full text textget Get text data entries textsearch Search the textual description of sequence(s) xmltext Get XML document original full text DATA RETRIEVAL TOOL DATA acdc Test an application ACD file acdpretty Correctly reformat an application ACD file acdtable Generate an HTML table of parameters from an application ACD file acdtrace Trace processing of an application ACD file (for testing) acdvalid Validate an application ACD file DATA RETRIEVAL URL DATA urlget Get URLs of data resources DATA RETRIEVAL XML DATA xmlget Get XML data DISPLAY abiview Display the trace in an ABI sequencer file cirdna Draw circular map of DNA constructs iep Calculate the isoelectric point of proteins lindna Draw linear maps of DNA constructs pepinfo Plot amino acid properties of a protein sequence in parallel pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence plotorf Plot potential open reading frames in a nucleotide sequence prettyplot Draw a sequence alignment with pretty formatting prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showfeat Display features of a sequence in pretty format showpep Display protein sequences with features in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs topo Draw an image of a transmembrane protein DOCUMENTATION seealso Find programs with similar function to a specified program tfm Display full documentation for an application wossdata Find programs by EDAM data wossinput Find programs by EDAM input data wossname Find programs by keywords in their short description wossoperation Find programs by EDAM operation wossoutput Find programs by EDAM output data wossparam Find programs by EDAM parameter wosstopic Find programs by EDAM topic EDIT aligncopy Read and write alignments aligncopypair Read and write pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Remove a section from a sequence degapseq Remove non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieve sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featcopy Read and write a feature table featmerge Merge two overlapping feature tables featreport Read and write a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences maskambignuc Mask all ambiguity characters in nucleotide sequences with N maskambigprot Mask all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Read and write (return) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Read and count sequences seqfraggle Remove fragment sequences from DHF files seqret Read and write (return) sequences seqretsetall Read and write (return) many sets of sequences seqretsplit Read sequences and write them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Read and write (return) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Remove vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file ENZYME KINETICS findkm Calculate and plot enzyme reaction data FEATURE TABLES extractfeat Extract features from sequence(s) maskfeat Write a sequence with masked features showfeat Display features of a sequence in pretty format twofeat Find neighbouring pairs of features in sequence(s) 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 libgen Generate discriminating elements from alignments 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 MENUS emnu Simple menu of EMBOSS applications NUCLEIC 2D STRUCTURE banana Plot bending and curvature data for B-DNA btwisted Calculate the twisting in a B-DNA sequence einverted Find inverted repeats in nucleotide sequences ovrnaalifold Calculate secondary structures for a set of aligned RNAs ovrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) ovrnacofold Calculate secondary structures of RNA dimers ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) ovrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) ovrnadistance Calculate distances between RNA secondary structures ovrnaduplex Predict RNA duplex (hybridization) sites and structure ovrnaeval Calculate energy of RNA sequences with a given secondary structu re ovrnaevalpair Calculate energy of RNA sequences on given secondary structure ovrnafold Calculate min. energy RNA structure / pair probabilities (partit ion) ovrnafoldpf Calculate min. energy RNA structure / pair probabilities ovrnaheat Calculate specific heat of RNA melting ovrnainverse Find RNA sequences with a given secondary structure ovrnalfold Calculate locally stable secondary structures of RNAs ovrnaplot Draw RNA secondary structures ovrnasubopt Calculate suboptimal secondary structure of RNA sirna Find siRNA duplexes in mRNA vrna2dfold Calculate RNA structures and samples of k,l neighbourhoods vrnaaliduplex RNA duplex calculation for two sequence alignments vrnaalifold Calculate secondary structures for a set of aligned RNAs vrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) vrnacofold Calculate secondary structures of RNA dimers vrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) vrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) vrnadistance Calculate distances between RNA secondary structures vrnaduplex Predict RNA duplex (hybridization) sites and structure vrnaeval Calculate energy of RNA sequences with a given secondary structu re vrnaevalpair Calculate energy of RNA sequences on given secondary structure vrnafold Calculate min. energy RNA secondary structures and pair probabil ities vrnafoldpf Calculate min. energy RNA structures / pair probabilities (parti tion) vrnaheat Calculate specific heat of RNA melting vrnainverse Find RNA sequences with a given secondary structure vrnalalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) vrnalfold Calculate locally stable secondary structures of RNAs vrnalfoldz Calculate locally stable secondary structures of RNAs plus zscor e vrnapkplex Calculate RNA structures plus pseudoknots vrnaplfold Compute avg. pair probabilities for local base pairs in RNA sequ ences vrnaplot Draw RNA secondary structures vrnasubopt Calculate suboptimal secondary structures of RNAs NUCLEIC CODON USAGE cai Calculate codon adaptation index chips Calculate Nc codon usage statistic codcmp Codon usage table comparison codcopy Copy and reformat a codon usage table cusp Create a codon usage table from nucleotide sequence(s) syco Draw synonymous codon usage statistic plot for a nucleotide sequence NUCLEIC COMPOSITION banana Plot bending and curvature data for B-DNA btwisted Calculate the twisting in a B-DNA sequence chaos Draw a chaos game representation plot for a nucleotide sequence compseq Calculate the composition of unique words in sequences dan Calculate nucleic acid melting temperature density Draw a nucleic acid density plot freak Generate residue/base frequency table or plot isochore Plot isochores in DNA sequences wordcount Count and extract unique words in molecular sequence(s) NUCLEIC CPG ISLANDS cpgplot Identify and plot CpG islands in nucleotide sequence(s) cpgreport Identify and report CpG-rich regions in nucleotide sequence(s) geecee Calculate fractional GC content of nucleic acid sequences newcpgreport Identify CpG islands in nucleotide sequence(s) newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s) NUCLEIC FUNCTIONAL SITES marscan Find matrix/scaffold recognition (MRS) signatures in DNA sequences sirna Find siRNA duplexes in mRNA trimest Remove poly-A tails from nucleotide sequences NUCLEIC GENE FINDING checktrans Report STOP codons and ORF statistics of a protein getorf Find and extract open reading frames (ORFs) marscan Find matrix/scaffold recognition (MRS) signatures in DNA sequences plotorf Plot potential open reading frames in a nucleotide sequence showorf Display a nucleotide sequence and translation in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs syco Draw synonymous codon usage statistic plot for a nucleotide sequence tcode Identify protein-coding regions using Fickett TESTCODE statistic wobble Plot third base position variability in a nucleotide sequence NUCLEIC MOTIFS dreg Regular expression search of nucleotide sequence(s) fuzznuc Search for patterns in nucleotide sequences fuzztran Search for patterns in protein sequences (translated) NUCLEIC MUTATION msbar Mutate a sequence shuffleseq Shuffle a set of sequences maintaining composition NUCLEIC PRIMERS eprimer3 Pick PCR primers and hybridization oligos eprimer32 Pick PCR primers and hybridization oligos primersearch Search DNA sequences for matches with primer pairs stssearch Search a DNA database for matches with a set of STS primers NUCLEIC PROFILES profit Scan one or more sequences with a simple frequency matrix prophecy Create frequency matrix or profile from a multiple alignment prophet Scan one or more sequences with a Gribskov or Henikoff profile NUCLEIC PROPERTIES banana Plot bending and curvature data for B-DNA btwisted Calculate the twisting in a B-DNA sequence dan Calculate nucleic acid melting temperature vrnaheat Calculate specific heat of RNA melting NUCLEIC REPEATS einverted Find inverted repeats in nucleotide sequences equicktandem Find tandem repeats in nucleotide sequences etandem Find tandem repeats in a nucleotide sequence palindrome Find inverted repeats in nucleotide sequence(s) NUCLEIC RESTRICTION recoder Find restriction sites to remove (mutate) with no translation change redata Retrieve information from REBASE restriction enzyme database remap Display restriction enzyme binding sites in a nucleotide sequence restover Find restriction enzymes producing a specific overhang restrict Report restriction enzyme cleavage sites in a nucleotide sequence showseq Display sequences with features in pretty format silent Find restriction sites to insert (mutate) with no translation change NUCLEIC RNA FOLDING ovrnaalifold Calculate secondary structures for a set of aligned RNAs ovrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) ovrnacofold Calculate secondary structures of RNA dimers ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) ovrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) ovrnadistance Calculate distances between RNA secondary structures ovrnaduplex Predict RNA duplex (hybridization) sites and structure ovrnaeval Calculate energy of RNA sequences with a given secondary structu re ovrnaevalpair Calculate energy of RNA sequences on given secondary structure ovrnafold Calculate min. energy RNA structure / pair probabilities (partit ion) ovrnafoldpf Calculate min. energy RNA structure / pair probabilities ovrnaheat Calculate specific heat of RNA melting ovrnainverse Find RNA sequences with a given secondary structure ovrnalfold Calculate locally stable secondary structures of RNAs ovrnaplot Draw RNA secondary structures ovrnasubopt Calculate suboptimal secondary structure of RNA vrna2dfold Calculate RNA structures and samples of k,l neighbourhoods vrnaaliduplex RNA duplex calculation for two sequence alignments vrnaalifold Calculate secondary structures for a set of aligned RNAs vrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) vrnacofold Calculate secondary structures of RNA dimers vrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) vrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) vrnadistance Calculate distances between RNA secondary structures vrnaduplex Predict RNA duplex (hybridization) sites and structure vrnaeval Calculate energy of RNA sequences with a given secondary structu re vrnaevalpair Calculate energy of RNA sequences on given secondary structure vrnafold Calculate min. energy RNA secondary structures and pair probabil ities vrnafoldpf Calculate min. energy RNA structures / pair probabilities (parti tion) vrnaheat Calculate specific heat of RNA melting vrnainverse Find RNA sequences with a given secondary structure vrnalalifoldpf Calculate secondary structures for a set of aligned RNAs (partit ion) vrnalfold Calculate locally stable secondary structures of RNAs vrnalfoldz Calculate locally stable secondary structures of RNAs plus zscor e vrnapkplex Calculate RNA structures plus pseudoknots vrnaplfold Compute avg. pair probabilities for local base pairs in RNA sequ ences vrnaplot Draw RNA secondary structures vrnasubopt Calculate suboptimal secondary structures of RNAs NUCLEIC TRANSCRIPTION jaspscan Scan DNA sequences for transcription factors marscan Find matrix/scaffold recognition (MRS) signatures in DNA sequences tfscan Identify transcription factor binding sites in DNA sequences NUCLEIC TRANSLATION backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence backtranseq Back-translate a protein sequence to a nucleotide sequence checktrans Report STOP codons and ORF statistics of a protein coderet Extract CDS, mRNA and translations from feature tables plotorf Plot potential open reading frames in a nucleotide sequence prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showorf Display a nucleotide sequence and translation in pretty format showseq Display sequences with features in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences ONTOLOGY ontocount Count ontology term(s) ontoget Get ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id ontogetobsolete Get ontology ontology terms ontogetroot Get ontology root terms by child identifier ontogetsibs Get ontology term(s) by id with common parent ontogetup Get ontology term(s) by id of child ontoisobsolete Report whether an ontology term id is obsolete ontotext Get ontology term(s) original full text ONTOLOGY EDAM drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource edamdef Find EDAM ontology terms by definition edamhasinput Find EDAM ontology terms by has_input relation edamhasoutput Find EDAM ontology terms by has_output relation edamisformat Find EDAM ontology terms by is_format_of relation edamisid Find EDAM ontology terms by is_identifier_of relation edamname Find EDAM ontology terms by name wossdata Find programs by EDAM data wossinput Find programs by EDAM input data wossoperation Find programs by EDAM operation wossoutput Find programs by EDAM output data wossparam Find programs by EDAM parameter wosstopic Find programs by EDAM topic ONTOLOGY GO godef Find GO ontology terms by definition goname Find GO ontology terms by name ONTOLOGY TAXONOMY taxget Get taxon(s) taxgetdown Get descendants of taxon(s) taxgetrank Get parents of taxon(s) taxgetspecies Get all species under taxon(s) taxgetup Get parents of taxon(s) PHYLOGENY CONSENSUS econsense Majority-rule and strict consensus tree fconsense Majority-rule and strict consensus tree ftreedist Calculate distances between trees ftreedistpair Calculate distance 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 Create a distance matrix from a multiple sequence alignment 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 Estimate 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 Calculate 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 Predict protein secondary structure using GOR method helixturnhelix Identify nucleic acid-binding motifs in protein sequences pepcoil Predict coiled coil regions in protein sequences pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence PROTEIN 3D STRUCTURE contacts Generate intra-chain CON files from CCF files 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 psiphi Calculates phi and psi torsion angles from protein coordinates PROTEIN COMPOSITION backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence backtranseq Back-translate a protein sequence to a nucleotide sequence compseq Calculate the composition of unique words in sequences emowse Search protein sequences by digest fragment molecular weight freak Generate residue/base frequency table or plot mwcontam Find weights common to multiple molecular weights files mwfilter Filter noisy data from molecular weights file oddcomp Identify proteins with specified sequence word composition pepdigest Report on protein proteolytic enzyme or reagent cleavage sites pepinfo Plot amino acid properties of a protein sequence in parallel pepstats Calculate statistics of protein properties wordcount Count and extract unique words in molecular sequence(s) PROTEIN DOMAINS cathparse Generate DCF file from raw CATH files domainalign Generate alignments (DAF file) for nodes in a DCF file domainnr Remove redundant domains from a DCF file domainrep Reorder DCF file to identify representative structures domainseqs Add sequence records to a DCF file domainsse Add secondary structure records to a DCF file helixturnhelix Identify nucleic acid-binding motifs in protein sequences libgen Generate discriminating elements from alignments matgen3d Generate a 3D-1D scoring matrix from CCF files pepcoil Predict coiled coil regions in protein sequences rocon Generate a hits file from comparing two DHF files rocplot Perform ROC analysis on hits files scopparse Generate DCF file from raw SCOP files seqalign Extend alignments (DAF file) with sequences (DHF file) seqfraggle Remove fragment sequences from DHF files seqsort Remove ambiguous classified sequences from DHF files seqwords Generate DHF files from keyword search of UniProt ssematch Search a DCF file for secondary structure matches PROTEIN FUNCTIONAL SITES echlorop Report presence of chloroplast transit peptides elipop Predict lipoproteins esignalp Report protein signal cleavage sites etmhmm Reports transmembrane helices sigcleave Report on signal cleavage sites in a protein sequence siggenlig Generate ligand-binding signatures from a CON file sigscan Generate hits (DHF file) from a signature search tmap Predict and plot transmembrane segments in protein sequences topo Draw an image of a transmembrane protein PROTEIN MODIFICATIONS enetnglyc Report N-glycosylation sites in human proteins enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins enetphos Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins eprop Report propeptide cleavage sites in proteins esignalp Report protein signal cleavage sites eyinoyang Report O-(beta)-GlcNAc attachment sites PROTEIN MOTIFS antigenic Find antigenic sites in proteins eiprscan Motif detection elipop Predict lipoproteins emast Motif detection ememe Multiple EM for motif elicitation ememetext Multiple EM for motif elicitation, text file only epestfind Find PEST motifs as potential proteolytic cleavage sites fuzzpro Search for patterns in protein sequences fuzztran Search for patterns in protein sequences (translated) omeme Motif detection patmatdb Search protein sequences with a sequence motif patmatmotifs Scan a protein sequence with motifs from the PROSITE database preg Regular expression search of protein sequence(s) pscan Scan protein sequence(s) with fingerprints from the PRINTS database sigcleave Report on signal cleavage sites in a protein sequence PROTEIN MUTATION msbar Mutate a sequence shuffleseq Shuffle a set of sequences maintaining composition PROTEIN PROFILES profit Scan one or more sequences with a simple frequency matrix prophecy Create frequency matrix or profile from a multiple alignment prophet Scan one or more sequences with a Gribskov or Henikoff profile seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file siggen Generate 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 and writes hits (LHF file) PROTEIN PROPERTIES charge Draw a protein charge plot hmoment Calculate and plot hydrophobic moment for protein sequence(s) iep Calculate the isoelectric point of proteins octanol Draw a White-Wimley protein hydropathy plot pepinfo Plot amino acid properties of a protein sequence in parallel pepstats Calculate statistics of protein properties pepwindow Draw a hydropathy plot for a protein sequence pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment TEST crystalball Answer every drug discovery question about a sequence UTILS embossdata Find and retrieve EMBOSS data files embossupdate Check for more recent updates to EMBOSS embossversion Report the current EMBOSS version number UTILS DATABASE CREATION aaindexextract Extract amino acid property data from AAINDEX allversusall Sequence similarity data from all-versus-all comparison cathparse Generate DCF file from raw CATH files cutgextract Extract codon usage tables from CUTG database domainer Generate domain CCF files from protein CCF files domainnr Remove redundant domains from a DCF file domainseqs Add sequence records to a DCF file domainsse Add secondary structure records to a DCF file hetparse Convert heterogen group dictionary to EMBL-like format jaspextract Extract data from JASPAR pdbparse Parse PDB files and writes protein CCF files pdbplus Add accessibility and secondary structure to a CCF file pdbtosp Convert swissprot:PDB codes file to EMBL-like format printsextract Extract data from PRINTS database for use by pscan prosextract Process the PROSITE motif database for use by patmatmotifs rebaseextract Process the REBASE database for use by restriction enzyme applica tions scopparse Generate DCF file from raw SCOP files seqnr Remove redundancy from DHF files sites Generate residue-ligand CON files from CCF files ssematch Search a DCF file for secondary structure matches tfextract Process TRANSFAC transcription factor database for use by tfscan UTILS DATABASE INDEXING dbiblast Index a BLAST database dbifasta Index a fasta file database dbiflat Index a flat file database dbigcg Index a GCG formatted database dbxcompress Compress an uncompressed dbx index dbxedam Index the EDAM ontology using b+tree indices dbxfasta Index a fasta file database using b+tree indices dbxflat Index a flat file database using b+tree indices dbxgcg Index a GCG formatted database using b+tree indices dbxobo Index an obo ontology using b+tree indices dbxreport Validate index and report internals for dbx databases dbxresource Index a data resource catalogue using b+tree indices dbxstat Dump statistics for dbx databases dbxtax Index NCBI taxonomy using b+tree indices dbxuncompress Uncompress a compressed dbx index Example 3 Display an alphabetic listing of all programs: % wossname -search "" -alphabetic Find programs by keywords in their short description ALPHABETIC LIST OF PROGRAMS aaindexextract Extract amino acid property data from AAINDEX abiview Display the trace in an ABI sequencer file acdc Test an application ACD file acdpretty Correctly reformat an application ACD file acdtable Generate an HTML table of parameters from an application ACD fi le acdtrace Trace processing of an application ACD file (for testing) acdvalid Validate an application ACD file aligncopy Read and write alignments aligncopypair Read and write pairs from alignments allversusall Sequence similarity data from all-versus-all comparison antigenic Find antigenic sites in proteins assemblyget Get assembly of sequence reads backtranambig Back-translate a protein sequence to ambiguous nucleotide seque nce backtranseq Back-translate a protein sequence to a nucleotide sequence banana Plot bending and curvature data for B-DNA biosed Replace or delete sequence sections btwisted Calculate the twisting in a B-DNA sequence cachedas Generate server cache file for DAS servers or for the DAS regis try cachedbfetch Generate server cache file for Dbfetch/WSDbfetch data sources cacheebeyesearch Generate server cache file for EB-eye search domains cacheensembl Generate server cache file for an Ensembl server cai Calculate codon adaptation index cathparse Generate DCF file from raw CATH files chaos Draw a chaos game representation plot for a nucleotide sequence charge Draw a protein charge plot checktrans Report STOP codons and ORF statistics of a protein chips Calculate Nc codon usage statistic cirdna Draw circular map of DNA constructs codcmp Codon usage table comparison codcopy Copy and reformat a codon usage table coderet Extract CDS, mRNA and translations from feature tables compseq Calculate the composition of unique words in sequences cons Create a consensus sequence from a multiple alignment consambig Create an ambiguous consensus sequence from a multiple alignmen t contacts Generate intra-chain CON files from CCF files cpgplot Identify and plot CpG islands in nucleotide sequence(s) cpgreport Identify and report CpG-rich regions in nucleotide sequence(s) crystalball Answer every drug discovery question about a sequence cusp Create a codon usage table from nucleotide sequence(s) cutgextract Extract codon usage tables from CUTG database cutseq Remove a section from a sequence dan Calculate nucleic acid melting temperature dbiblast Index a BLAST database dbifasta Index a fasta file database dbiflat Index a flat file database dbigcg Index a GCG formatted database dbtell Display information about a public database dbxcompress Compress an uncompressed dbx index dbxedam Index the EDAM ontology using b+tree indices dbxfasta Index a fasta file database using b+tree indices dbxflat Index a flat file database using b+tree indices dbxgcg Index a GCG formatted database using b+tree indices dbxobo Index an obo ontology using b+tree indices dbxreport Validate index and report internals for dbx databases dbxresource Index a data resource catalogue using b+tree indices dbxstat Dump statistics for dbx databases dbxtax Index NCBI taxonomy using b+tree indices dbxuncompress Uncompress a compressed dbx index degapseq Remove non-alphabetic (e.g. gap) characters from sequences density Draw a nucleic acid density plot descseq Alter the name or description of a sequence diffseq Compare and report features of two similar sequences distmat Create a distance matrix from a multiple sequence alignment domainalign Generate alignments (DAF file) for nodes in a DCF file domainer Generate domain CCF files from protein CCF files domainnr Remove redundant domains from a DCF file domainrep Reorder DCF file to identify representative structures domainreso Remove low resolution domains from a DCF file domainseqs Add sequence records to a DCF file domainsse Add secondary structure records to a DCF file dotmatcher Draw a threshold dotplot of two sequences dotpath Draw a non-overlapping wordmatch dotplot of two sequences dottup Display a wordmatch dotplot of two sequences dreg Regular expression search of nucleotide sequence(s) drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource drget Get data resource entries drtext Get data resource entries complete text echlorop Report presence of chloroplast transit peptides eclique Largest clique program econsense Majority-rule and strict consensus tree econtml Continuous character maximum likelihood method econtrast Continuous character contrasts edamdef Find EDAM ontology terms by definition edamhasinput Find EDAM ontology terms by has_input relation edamhasoutput Find EDAM ontology terms by has_output relation edamisformat Find EDAM ontology terms by is_format_of relation edamisid Find EDAM ontology terms by is_identifier_of relation edamname Find EDAM ontology terms by name 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 Find inverted repeats in nucleotide sequences eiprscan Motif detection ekitsch Fitch-Margoliash method with contemporary tips elipop Predict lipoproteins emast Motif detection embossdata Find and retrieve EMBOSS data files embossupdate Check for more recent updates to EMBOSS embossversion Report the current EMBOSS version number ememe Multiple EM for motif elicitation ememetext Multiple EM for motif elicitation, text file only emira MIRA fragment assembly program emiraest MIRAest fragment assembly program emix Mixed parsimony algorithm emma Multiple sequence alignment (ClustalW wrapper) emnu Simple menu of EMBOSS applications emowse Search protein sequences by digest fragment molecular weight eneighbor Phylogenies from distance matrix by N-J or UPGMA method enetnglyc Report N-glycosylation sites in human proteins enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian pr oteins enetphos Report Ser, Thr and Tyr phosphorylation sites in eukaryotic pro teins entret Retrieve sequence entries from flatfile databases and files eomega Multiple sequence alignment (ClustalO wrapper) eomegapp Profile with profile (ClustalO wrapper) eomegaps Single sequence with profile (ClustalO wrapper) eomegash Sequence with HMM (ClustalO wrapper) eomegasp Sequence with profile (ClustalO wrapper) epenny Penny algorithm, branch-and-bound epestfind Find PEST motifs as potential proteolytic cleavage sites eprimer3 Pick PCR primers and hybridization oligos eprimer32 Pick PCR primers and hybridization oligos eprop Report propeptide cleavage sites in proteins eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm equicktandem Find tandem repeats in nucleotide sequences erestml Restriction site maximum likelihood method eseqboot Bootstrapped sequences algorithm esignalp Report protein signal cleavage sites esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST sequences to genomic DNA sequence etandem Find tandem repeats in a nucleotide sequence etmhmm Reports transmembrane helices extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence eyinoyang Report O-(beta)-GlcNAc attachment sites 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 Estimate 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 featcopy Read and write a feature table featmerge Merge two overlapping feature tables featreport Read and write a feature table feattext Return a feature table original text 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 Calculate and plot enzyme reaction data 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 Generate residue/base frequency table or plot frestboot Bootstrapped restriction sites algorithm frestdist Calculate 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 Calculate distances between trees ftreedistpair Calculate distance between two sets of trees fuzznuc Search for patterns in nucleotide sequences fuzzpro Search for patterns in protein sequences fuzztran Search for patterns in protein sequences (translated) garnier Predict protein secondary structure using GOR method geecee Calculate fractional GC content of nucleic acid sequences getorf Find and extract open reading frames (ORFs) godef Find GO ontology terms by definition goname Find GO ontology terms by name helixturnhelix Identify nucleic acid-binding motifs in protein sequences hetparse Convert heterogen group dictionary to EMBL-like format hmoment Calculate and plot hydrophobic moment for protein sequence(s) iep Calculate the isoelectric point of proteins infoalign Display basic information about a multiple sequence alignment infoassembly Display information about assemblies infobase Return information on a given nucleotide base inforesidue Return information on a given amino acid residue infoseq Display basic information about sequences interface Generate inter-chain CON files from CCF files isochore Plot isochores in DNA sequences jaspextract Extract data from JASPAR jaspscan Scan DNA sequences for transcription factors libgen Generate discriminating elements from alignments lindna Draw linear maps of DNA constructs listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences marscan Find matrix/scaffold recognition (MRS) signatures in DNA sequen ces maskambignuc Mask all ambiguity characters in nucleotide sequences with N maskambigprot Mask all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions matcher Waterman-Eggert local alignment of two sequences matgen3d Generate a 3D-1D scoring matrix from CCF files megamerger Merge two large overlapping DNA sequences merger Merge two overlapping sequences msbar Mutate a sequence mse Multiple sequence editor mwcontam Find weights common to multiple molecular weights files mwfilter Filter noisy data from molecular weights file needle Needleman-Wunsch global alignment of two sequences needleall Many-to-many pairwise alignments of two sequence sets newcpgreport Identify CpG islands in nucleotide sequence(s) newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s) newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequenc es nthseqset Read and write (return) one set of sequences from many oalistat Statistics for multiple alignment files octanol Draw a White-Wimley protein hydropathy plot oddcomp Identify proteins with specified sequence word 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 ontocount Count ontology term(s) ontoget Get ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id ontogetobsolete Get ontology ontology terms ontogetroot Get ontology root terms by child identifier ontogetsibs Get ontology term(s) by id with common parent ontogetup Get ontology term(s) by id of child ontoisobsolete Report whether an ontology term id is obsolete ontotext Get ontology term(s) original full text ovrnaalifold Calculate secondary structures for a set of aligned RNAs ovrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (parti tion) ovrnacofold Calculate secondary structures of RNA dimers ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) ovrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) ovrnadistance Calculate distances between RNA secondary structures ovrnaduplex Predict RNA duplex (hybridization) sites and structure ovrnaeval Calculate energy of RNA sequences with a given secondary struct ure ovrnaevalpair Calculate energy of RNA sequences on given secondary structure ovrnafold Calculate min. energy RNA structure / pair probabilities (parti tion) ovrnafoldpf Calculate min. energy RNA structure / pair probabilities ovrnaheat Calculate specific heat of RNA melting ovrnainverse Find RNA sequences with a given secondary structure ovrnalfold Calculate locally stable secondary structures of RNAs ovrnaplot Draw RNA secondary structures ovrnasubopt Calculate suboptimal secondary structure of RNA palindrome Find inverted repeats in nucleotide sequence(s) pasteseq Insert one sequence into another patmatdb Search protein sequences with a sequence motif patmatmotifs Scan a protein sequence with motifs from the PROSITE database pdbparse Parse PDB files and writes protein CCF files pdbplus Add accessibility and secondary structure to a CCF file pdbtosp Convert swissprot:PDB codes file to EMBL-like format pepcoil Predict coiled coil regions in protein sequences pepdigest Report on protein proteolytic enzyme or reagent cleavage sites pepinfo Plot amino acid properties of a protein sequence in parallel pepnet Draw a helical net for a protein sequence pepstats Calculate statistics of protein properties pepwheel Draw a helical wheel diagram for a protein sequence pepwindow Draw a hydropathy plot for a protein sequence pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment plotcon Plot conservation of a sequence alignment plotorf Plot potential open reading frames in a nucleotide sequence polydot Draw dotplots for all-against-all comparison of a sequence set preg Regular expression search of protein sequence(s) prettyplot Draw a sequence alignment with pretty formatting prettyseq Write a nucleotide sequence and its translation to file primersearch Search DNA sequences for matches with primer pairs printsextract Extract data from PRINTS database for use by pscan profit Scan one or more sequences with a simple frequency matrix prophecy Create frequency matrix or profile from a multiple alignment prophet Scan one or more sequences with a Gribskov or Henikoff profile prosextract Process the PROSITE motif database for use by patmatmotifs pscan Scan protein sequence(s) with fingerprints from the PRINTS data base psiphi Calculates phi and psi torsion angles from protein coordinates rebaseextract Process the REBASE database for use by restriction enzyme appli cations recoder Find restriction sites to remove (mutate) with no translation c hange redata Retrieve information from REBASE restriction enzyme database refseqget Get reference sequence remap Display restriction enzyme binding sites in a nucleotide sequen ce restover Find restriction enzymes producing a specific overhang restrict Report restriction enzyme cleavage sites in a nucleotide sequen ce revseq Reverse and complement a nucleotide sequence rocon Generate a hits file from comparing two DHF files rocplot Perform ROC analysis on hits files scopparse Generate DCF file from raw SCOP files seealso Find programs with similar function to a specified program seqalign Extend alignments (DAF file) with sequences (DHF file) seqcount Read and count sequences seqfraggle Remove fragment sequences from DHF files seqmatchall All-against-all word comparison of a sequence set seqnr Remove redundancy from DHF files seqret Read and write (return) sequences seqretsetall Read and write (return) many sets of sequences seqretsplit Read sequences and write them to individual files seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file seqsort Remove ambiguous classified sequences from DHF files seqwords Generate DHF files from keyword search of UniProt seqxref Retrieve all database cross-references for a sequence entry seqxrefget Retrieve all cross-referenced data for a sequence entry servertell Display information about a public server showalign Display a multiple sequence alignment in pretty format showdb Display information on configured databases showfeat Display features of a sequence in pretty format showorf Display a nucleotide sequence and translation in pretty format showpep Display protein sequences with features in pretty format showseq Display sequences with features in pretty format showserver Display information on configured servers shuffleseq Shuffle a set of sequences maintaining composition sigcleave Report on signal cleavage sites in a protein sequence siggen Generate 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 and writes hits (LHF file) silent Find restriction sites to insert (mutate) with no translation c hange sirna Find siRNA duplexes in mRNA sites Generate residue-ligand CON files from CCF files sixpack Display a DNA sequence with 6-frame translation and ORFs sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Read and write (return) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences ssematch Search a DCF file for secondary structure matches stretcher Needleman-Wunsch rapid global alignment of two sequences stssearch Search a DNA database for matches with a set of STS primers supermatcher Calculate approximate local pair-wise alignments of larger sequ ences syco Draw synonymous codon usage statistic plot for a nucleotide seq uence taxget Get taxon(s) taxgetdown Get descendants of taxon(s) taxgetrank Get parents of taxon(s) taxgetspecies Get all species under taxon(s) taxgetup Get parents of taxon(s) tcode Identify protein-coding regions using Fickett TESTCODE statisti c textget Get text data entries textsearch Search the textual description of sequence(s) tfextract Process TRANSFAC transcription factor database for use by tfsca n tfm Display full documentation for an application tfscan Identify transcription factor binding sites in DNA sequences tmap Predict and plot transmembrane segments in protein sequences topo Draw an image of a transmembrane protein tranalign Generate an alignment of nucleic coding regions from aligned pr oteins transeq Translate nucleic acid sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file twofeat Find neighbouring pairs of features in sequence(s) union Concatenate multiple sequences into a single sequence urlget Get URLs of data resources variationget Get sequence variations vectorstrip Remove vectors from the ends of nucleotide sequence(s) vrna2dfold Calculate RNA structures and samples of k,l neighbourhoods vrnaaliduplex RNA duplex calculation for two sequence alignments vrnaalifold Calculate secondary structures for a set of aligned RNAs vrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (parti tion) vrnacofold Calculate secondary structures of RNA dimers vrnacofoldconc Calculate secondary structures of RNA dimers (concentrations) vrnacofoldpf Calculate secondary structures of RNA dimers (partitioning) vrnadistance Calculate distances between RNA secondary structures vrnaduplex Predict RNA duplex (hybridization) sites and structure vrnaeval Calculate energy of RNA sequences with a given secondary struct ure vrnaevalpair Calculate energy of RNA sequences on given secondary structure vrnafold Calculate min. energy RNA secondary structures and pair probabi lities vrnafoldpf Calculate min. energy RNA structures / pair probabilities (part ition) vrnaheat Calculate specific heat of RNA melting vrnainverse Find RNA sequences with a given secondary structure vrnalalifoldpf Calculate secondary structures for a set of aligned RNAs (parti tion) vrnalfold Calculate locally stable secondary structures of RNAs vrnalfoldz Calculate locally stable secondary structures of RNAs plus zsco re vrnapkplex Calculate RNA structures plus pseudoknots vrnaplfold Compute avg. pair probabilities for local base pairs in RNA seq uences vrnaplot Draw RNA secondary structures vrnasubopt Calculate suboptimal secondary structures of RNAs water Smith-Waterman local alignment of sequences whichdb Search all sequence databases for an entry and retrieve it wobble Plot third base position variability in a nucleotide sequence wordcount Count and extract unique words in molecular sequence(s) wordfinder Match large sequences against one or more other sequences wordmatch Find regions of identity (exact matches) of two sequences wossdata Find programs by EDAM data wossinput Find programs by EDAM input data wossname Find programs by keywords in their short description wossoperation Find programs by EDAM operation wossoutput Find programs by EDAM output data wossparam Find programs by EDAM parameter wosstopic Find programs by EDAM topic xmlget Get XML data xmltext Get XML document original full text yank Add a sequence reference (a full USA) to a list file Example 4 Display only the groups that the programs can belong to: % wossname -search "" -groups Find programs by keywords in their short description ACD ALIGNMENT ALIGNMENT CONSENSUS ALIGNMENT DIFFERENCES ALIGNMENT DOT PLOTS ALIGNMENT GLOBAL ALIGNMENT LOCAL ALIGNMENT MULTIPLE ASSEMBLY FRAGMENT ASSEMBLY DATA RESOURCES DATA RETRIEVAL DATA RETRIEVAL CHEMISTRY DATA DATA RETRIEVAL FEATURE DATA DATA RETRIEVAL ONTOLOGY DATA DATA RETRIEVAL RESOURCE DATA DATA RETRIEVAL SEQUENCE DATA DATA RETRIEVAL SEQUENCE DATA ASSEMBLY DATA DATA RETRIEVAL TEXT DATA DATA RETRIEVAL TOOL DATA DATA RETRIEVAL URL DATA DATA RETRIEVAL XML DATA DISPLAY DOCUMENTATION EDIT ENZYME KINETICS FEATURE TABLES HMM MENUS NUCLEIC 2D STRUCTURE NUCLEIC CODON USAGE NUCLEIC COMPOSITION NUCLEIC CPG ISLANDS NUCLEIC FUNCTIONAL SITES NUCLEIC GENE FINDING NUCLEIC MOTIFS NUCLEIC MUTATION NUCLEIC PRIMERS NUCLEIC PROFILES NUCLEIC PROPERTIES NUCLEIC REPEATS NUCLEIC RESTRICTION NUCLEIC RNA FOLDING NUCLEIC TRANSCRIPTION NUCLEIC TRANSLATION ONTOLOGY ONTOLOGY EDAM ONTOLOGY GO ONTOLOGY TAXONOMY 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 DOMAINS PROTEIN FUNCTIONAL SITES PROTEIN MODIFICATIONS PROTEIN MOTIFS PROTEIN MUTATION PROTEIN PROFILES PROTEIN PROPERTIES TEST UTILS UTILS DATABASE CREATION UTILS DATABASE INDEXING Example 5 Output html tags around the list of programs: % wossname "" -html -out wossname.html Find programs by keywords in their short description Go to the output files for this example Command line arguments Find programs by keywords in their short description Version: EMBOSS:6.6.0.0 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) 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] Tool metadata output file -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 be 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) -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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 -version boolean Report version number and exit Input file format 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. Output file format The results are written out as a simple list preceded by the group that the programs belong to or the word that is being searched for. Output files for usage example 5 File: wossname.html

ACD

Program name Description
acdc Test an application ACD file
acdpretty Correctly reformat an application ACD file
acdtable Generate an HTML table of parameters from an application ACD file
acdtrace Trace processing of an application ACD file (for testing)
acdvalid Validate an application ACD file

ALIGNMENT

Program name Description
extractalign Extract regions from a sequence alignment

ALIGNMENT CONSENSUS

[Part of this file has been deleted for brevity]
Program name Description
cons Create a consensus sequence from a multiple alignment
dbxedam Index the EDAM ontology using b+tree indices
dbxfasta Index a fasta file database using b+tree indices
dbxflat Index a flat file database using b+tree indices
dbxgcg Index a GCG formatted database using b+tree indices
dbxobo Index an obo ontology using b+tree indices
dbxreport Validate index and report internals for dbx databases
dbxresource Index a data resource catalogue using b+tree indices
dbxstat Dump statistics for dbx databases
dbxtax Index NCBI taxonomy using b+tree indices
dbxuncompress Uncompress a compressed dbx index
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 , , and 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. Data files As noted above, the program ACD files are searched. The average user will not need to worry about this. Notes wossname reads the short descriptions and the program groups from the program ACD files. These file describe the command-line interface of the applications. You don't need to know about them unless you are writing EMBOSS programs. They are described in the EMBOSS Developers Manual. If a program's ACD file does not specify a program group, then it will be automatically assigned to the group ASSORTED in the output file. A program can belong to more than one group. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0 Known bugs None. See also Program name Description seealso Find programs with similar function to a specified program tfm Display full documentation for an application wossdata Find programs by EDAM data wossinput Find programs by EDAM input data wossoperation Find programs by EDAM operation wossoutput Find programs by EDAM output data wossparam Find programs by EDAM parameter wosstopic Find programs by EDAM topic Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None