tfm

Function

Description

The contributors of the EMBOSS programs do attempt to provide an adequate description of the programs. This documentation for your current release is included as HTML pages in the EMBOSS distribution and may be available at your site. The latest documentation for the next release is provided by the developers at http://emboss.sourceforge.net/apps/

The release documentation is also available however through the program tfm as normal text.

If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@embnet.org).

The unusual name of this program comes from the common computing science expression: RTFM. This acronym, as you probably already know, stands for Read The Fine* Manual; so this is The Fine* Manual.

* Insert the expletive of your choice here!

Paged text output to the screen

The text is paged to the screen using the UNIX program 'more'. The program 'more' is a very standard way for text files to be displayed in UNIX. You might, however, prefer the text to be displayed using other programs, for example 'less' (which has more functionality than 'more' and is used by many people). The UNIX environment variable 'PAGER' can be set to hold the name of your preferred program. If you have PAGER set, then tfm will use this specified program instead of using the default 'more' program. (If you want tfm to use a specified program that is different to the normal 'PAGER' program, then 'PAGER' can be overriden by setting the environment variable 'EMBOSS_PAGER' to hold the name of the program that should only be used to display text in tfm).

'PAGER' can be set in UNIX by a command like:
setenv PAGER less

To get help on 'more' when using it to display text, press the '?' key.
To get help on 'less' when using it to display text, press the 'h' key.

Usage

% tfm wossname Displays a program's help documentation manual wossname Function Finds programs by keywords in their one-line documentation Description This allows a user to search for keywords or parts of words in the brief documentation (as displayed by a program when it first starts). The program name and the brief description is output. If no words to search for are specified, then details of all the EMBOSS programs are output. 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. Usage Here is a sample session with wossname 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 remap Display sequence with restriction sites, translation etc restover Find restriction enzymes producing specific overhang restrict Finds restriction enzyme cleavage sites 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 nucleic acid 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 alignrunner Align sequence pairs in a directory comparator Compare contact scores of two sequence alignments contactalign Damian Counsell's experimental 2.5-D alignment algorithm esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST and genomic DNA sequences nawalign Damian Counsell's NW implementation nawalignrunner Nawalign all sequence pairs in a directory needle Needleman-Wunsch global alignment needlerunner Needle all sequence pairs in a directory scorer Score alignments using structural alignments scorerrunner SCORER for ordered pairs of substituted seqs stretcher Finds the best global alignment between two sequences substitute Substitute matches into a template substituterunner Run SUBSTITUTE on a directory of traces 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 wordmatch Finds all exact matches of a given size between 2 sequences ALIGNMENT MULTIPLE 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 degapseqrunner Degapseq all sequence pairs in a directory descseq Alter the name or description of a sequence entret Reads and writes (returns) flatfile entries 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 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 ealistat Statistics for multiple alignment files ehmmalign Align sequences with an HMM ehmmbuild Build HMM ehmmcalibrate Calibrate a hidden Markov model ehmmconvert Convert between HMM formats ehmmemit Extract HMM sequences ehmmfetch Extract HMM from a database ehmmindex Index an HMM database ehmmpfam Align single sequence with an HMM ehmmsearch 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 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 TRANSCRIPTION tfscan Scans DNA sequences for transcription factors NUCLEIC TRANSLATION 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 distmat Creates a distance matrix from multiple alignments 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 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 pasimony 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 contactcount Count specific versus non-specific contacts 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 scorecmapdir Contact scores for cleaned protein chain contact 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 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 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 meme Motif detection oddcomp Find protein sequence regions with a biased composition 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 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 alignrunner Align sequence pairs in a directory allversusall Sequence similarity data from all-versus-all comparison antigenic Finds antigenic sites in proteins 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 comparator Compare contact scores of two sequence alignments compseq Count composition of dimer/trimer/etc words in a sequence cons Creates a consensus from multiple alignments contactalign Damian Counsell's experimental 2.5-D alignment algorithm contactcount Count specific versus non-specific contacts 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 degapseqrunner Degapseq all sequence pairs in a directory 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 ealistat Statistics for multiple alignment files eclique Largest clique program econsense Majority-rule and strict consensus tree econtml Continuous character Maximum Likelihood method econtrast Continuous character Contrasts 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 with an HMM ehmmbuild Build HMM ehmmcalibrate Calibrate a hidden Markov model ehmmconvert Convert between HMM formats ehmmemit Extract HMM sequences ehmmfetch Extract HMM from a database ehmmindex Index an HMM database ehmmpfam Align single sequence with an HMM ehmmsearch Search sequence database with an HMM einverted Finds DNA inverted repeats ekitsch Fitch-Margoliash method with contemporary tips embossdata Finds or fetches data files read by EMBOSS programs embossversion Writes the current EMBOSS version number 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 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 pasimony 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 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 meme Motif detection merger Merge two overlapping nucleic acid 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 nawalign Damian Counsell's NW implementation nawalignrunner Nawalign all sequence pairs in a directory needle Needleman-Wunsch global alignment needlerunner Needle all sequence pairs in a directory 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 octanol Displays protein hydropathy oddcomp Find protein sequence regions with a biased composition 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 scorecmapdir Contact scores for cleaned protein chain contact files scorer Score alignments using structural alignments scorerrunner SCORER for ordered pairs of substituted seqs 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 substitute Substitute matches into a template substituterunner Run SUBSTITUTE on a directory of traces 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 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 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 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 program groups: % wossname -groups -html -prelink '#' Finds programs by keywords in their one-line documentation Keyword to search for, or blank to list all programs: * 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 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 6 Output html tags around the list of programs: % wossname '' -html -prelink 'http://emboss.sf.net/apps/' -postlink '.html' -ou t wossname.html Finds programs by keywords in their one-line documentation Go to the output files for this example Command line arguments 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 of all of the EMBOSS programs. If no keyword is specified, all programs will be listed. Additional (Optional) qualifiers (* if not always prompted): -explode boolean 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'. -outfile outfile Output file name -html toggle If you are sending the output to a file, this will format it for displaying as a table in a WWW document. * -prelink string If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps /programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps / here, then the first half of the URL before the programname will be set. * -postlink string If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps /programname.html then if you enter '.html' here, the second half of the URL after the programname will be set. -groups boolean If you use this option, then only the group names will output to the file -alphabetic boolean 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 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 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 -colon boolean 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 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 deaths 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 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 -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 -prelink If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the programname will be set. Any string is accepted An empty string is accepted -postlink If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter '.html' here, the second half of the URL after the programname will be set. Any string is accepted An empty string is accepted -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 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 6 File: wossname.html ACD Program name Description 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 Program name Description cons Creates a consensus from multiple alignments megamerger Merge two large overlapping nucleic acid sequences merger Merge two overlapping nucleic acid sequences ALIGNMENT DIFFERENCES Program name Description diffseq Find differences between nearly identical sequences ALIGNMENT DOT PLOTS Program name Description 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 Program name Description alignrunner Align sequence pairs in a directory comparator Compare contact scores of two sequence alignments contactalign Damian Counsell's experimental 2.5-D alignment algorithm esim4 Align an mRNA to a genomic DNA sequence est2genome Align EST and genomic DNA sequences nawalign Damian Counsell's NW implementation nawalignrunner Nawalign all sequence pairs in a directory needle Needleman-Wunsch global alignment needlerunner Needle all sequence pairs in a directory scorer Score alignments using structural alignments scorerrunner SCORER for ordered pairs of substituted seqs stretcher Finds the best global alignment between two sequences substitute Substitute matches into a template substituterunner Run SUBSTITUTE on a directory of traces ALIGNMENT LOCAL Program name Description [Part of this file has been deleted for brevity] profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles TEST Program name Description crystalball Answers every drug discovery question about a sequence myseq Demonstration of sequence reading UTILS DATABASE CREATION Program name Description 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 Program name Description 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 Program name Description embossdata Finds or fetches data files read by EMBOSS programs embossversion Writes the current EMBOSS version number 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 If a program's ACD file does not assign the program to a group, it will be automatically assigned to the group 'ASSORTED'. 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. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0 Known bugs None. See also 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 Author(s) Gary Williams (gwilliam © rfcgr.mrc.ac.uk) MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None

Command line arguments

   Standard (Mandatory) qualifiers:
  [-program]           string     Enter the name of an EMBOSS program

   Additional (Optional) qualifiers:
   -outfile            outfile    Output file name
   -html               boolean    This will format the output for displaying
                                  as a WWW document.
   -more               boolean    This uses the standard UNIX utility 'more'
                                  to display the text page-by-page, waiting
                                  for you to read one screen-full before going
                                  on to the next page. When you have finished
                                  reading a page, press the SPACE bar to
                                  proceed to the next page.

   Advanced (Unprompted) qualifiers: (none)
   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 deaths

Standard (Mandatory) qualifiers		Allowed values	Default
[-program] (Parameter 1)	Enter the name of an EMBOSS program	A string of at least 1 characters	Required
Additional (Optional) qualifiers		Allowed values	Default
-outfile	Output file name	Output file	stdout
-html	This will format the output for displaying as a WWW document.	Boolean value Yes/No	No
-more	This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page.	Boolean value Yes/No	@(!$(html))
Advanced (Unprompted) qualifiers		Allowed values	Default
(none)

Input file format

Output file format

The table of command line arguments can be a bit difficult to read. This is the result of changing HTML Web pages to text.

You will see a page of documentation on the wossname program. To see further pages, you should press the SPACE bar on your keyboard. To stop seeing the documentation before you get to the end of the text, you can press the key q to quit.

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments