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tfm |
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
Displays full documentation for an applicationDescription
tfm displays help information for the specified EMBOSS program.
Usage
Here is a sample session with tfm
% tfm wossname
Displays full documentation for an application
::::::::::::::
/homes/pmr/local/share/EMBOSS/doc/programs/text/wossname.txt
::::::::::::::
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
Finds 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
Finds programs by keywords in their short description
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
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 Displays 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 ""
Finds 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 Displays 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 Finds 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)
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 Generates server cache file for DAS servers or for the DAS regi
stry
cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch Generates server cache file for EB-eye search domains
dbtell Display information about a public database
servertell Display information about a public server
showdb Displays information on configured databases
showserver Displays information on configured servers
DATA RETRIEVAL
codcopy Copy and reformat a codon usage table
seqret Reads and writes (returns) 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 Reads and writes a feature table
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 Retrieves 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
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
whichdb Search all sequence databases for an entry and retrieve it
DATA RETRIEVAL TEXT DATA
drtext Get data resource entries complete text
entret Retrieves 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)
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
DISPLAY
abiview Display the trace in an ABI sequencer file
cirdna Draws circular maps of DNA constructs
iep Calculate the isoelectric point of proteins
lindna Draws 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 Displays protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
topo Draws an image of a transmembrane protein
DOCUMENTATION
seealso Finds programs with similar function to a specified program
tfm Displays full documentation for an application
wossdata Finds programs by EDAM data
wossinput Finds programs by EDAM input data
wossname Finds programs by keywords in their short description
wossoperation Finds programs by EDAM operation
wossoutput Finds programs by EDAM output data
wossparam Finds programs by EDAM parameter
wosstopic Finds programs by EDAM topic
EDIT
aligncopy Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Removes a section from a sequence
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieves 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 Reads and writes a feature table
featreport Reads and writes 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 Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks 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 Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Reads and counts sequences
seqfraggle Removes fragment sequences from DHF files
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of sequences
seqretsplit Reads sequences and writes them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) 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 Removes 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 Finds 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 Finds inverted repeats in nucleotide sequences
ovrnaalifold RNA alignment folding
ovrnaalifoldpf RNA alignment folding with partition
ovrnacofold RNA cofolding
ovrnacofoldconc RNA cofolding with concentrations
ovrnacofoldpf RNA cofolding with partitioning
ovrnadistance RNA distances
ovrnaduplex RNA duplex calculation
ovrnaeval RNA eval
ovrnaevalpair RNA eval with cofold
ovrnafold Calculate secondary structures of RNAs
ovrnafoldpf Secondary structures of RNAs with partition
ovrnaheat RNA melting
ovrnainverse RNA sequences matching a structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Plot vrnafold output
ovrnasubopt Calculate RNA suboptimals
sirna Finds siRNA duplexes in mRNA
vrna2dfold Structures and samples of k,l neighbourhoods
vrnaaliduplex RNA duplex calculation for two sequence alignments
vrnaalifold RNA alignment folding
vrnaalifoldpf RNA alignment folding with partition
vrnacofold RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf RNA cofolding with partitioning
vrnadistance RNA distances
vrnaduplex RNA duplex calculation
vrnaeval RNA eval
vrnaevalpair RNA eval with cofold
vrnafold Calculate secondary structures of RNAs
vrnafoldpf Secondary structures of RNAs with partition
vrnaheat RNA melting
vrnainverse RNA sequences matching a structure
vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Locally stable secondary structures of RNAs plus zscore
vrnapkplex RNA structures plus pseudoknots
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals
NUCLEIC CODON USAGE
cai Calculate codon adaptation index
chips Calculates 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 Calculates nucleic acid melting temperature
density Draw a nucleic acid density plot
freak Generate residue/base frequency table or plot
isochore Plots 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 Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
sirna Finds siRNA duplexes in mRNA
trimest Remove poly-A tails from nucleotide sequences
NUCLEIC GENE FINDING
checktrans Reports STOP codons and ORF statistics of a protein
getorf Finds and extracts open reading frames (ORFs)
marscan Finds 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 Shuffles a set of sequences maintaining composition
NUCLEIC PRIMERS
eprimer3 Picks PCR primers and hybridization oligos
eprimer32 Picks 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 Calculates nucleic acid melting temperature
vrnaheat RNA melting
NUCLEIC REPEATS
einverted Finds inverted repeats in nucleotide sequences
equicktandem Finds tandem repeats in nucleotide sequences
etandem Finds tandem repeats in a nucleotide sequence
palindrome Finds 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 Displays sequences with features in pretty format
silent Find restriction sites to insert (mutate) with no translation change
NUCLEIC RNA FOLDING
ovrnaalifold RNA alignment folding
ovrnaalifoldpf RNA alignment folding with partition
ovrnacofold RNA cofolding
ovrnacofoldconc RNA cofolding with concentrations
ovrnacofoldpf RNA cofolding with partitioning
ovrnadistance RNA distances
ovrnaduplex RNA duplex calculation
ovrnaeval RNA eval
ovrnaevalpair RNA eval with cofold
ovrnafold Calculate secondary structures of RNAs
ovrnafoldpf Secondary structures of RNAs with partition
ovrnaheat RNA melting
ovrnainverse RNA sequences matching a structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Plot vrnafold output
ovrnasubopt Calculate RNA suboptimals
vrna2dfold Structures and samples of k,l neighbourhoods
vrnaaliduplex RNA duplex calculation for two sequence alignments
vrnaalifold RNA alignment folding
vrnaalifoldpf RNA alignment folding with partition
vrnacofold RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf RNA cofolding with partitioning
vrnadistance RNA distances
vrnaduplex RNA duplex calculation
vrnaeval RNA eval
vrnaevalpair RNA eval with cofold
vrnafold Calculate secondary structures of RNAs
vrnafoldpf Secondary structures of RNAs with partition
vrnaheat RNA melting
vrnainverse RNA sequences matching a structure
vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Locally stable secondary structures of RNAs plus zscore
vrnapkplex RNA structures plus pseudoknots
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals
NUCLEIC TRANSCRIPTION
jaspscan Scans DNA sequences for transcription factors
marscan Finds 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 Reports 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 Displays 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 Finds programs by EDAM data
wossinput Finds programs by EDAM input data
wossoperation Finds programs by EDAM operation
wossoutput Finds programs by EDAM output data
wossparam Finds programs by EDAM parameter
wosstopic Finds 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 Distances between trees
ftreedistpair Distances between two sets of trees
PHYLOGENY CONTINUOUS CHARACTERS
econtml Continuous character Maximum Likelihood method
econtrast Continuous character contrasts
fcontrast Continuous character Contrasts
PHYLOGENY DISCRETE CHARACTERS
eclique Largest clique program
edollop Dollo and polymorphism parsimony algorithm
edolpenny Penny algorithm Dollo or polymorphism
efactor Multistate to binary recoding program
emix Mixed parsimony algorithm
epenny Penny algorithm, branch-and-bound
fclique Largest clique program
fdollop Dollo and polymorphism parsimony algorithm
fdolpenny Penny algorithm Dollo or polymorphism
ffactor Multistate to binary recoding program
fmix Mixed parsimony algorithm
fmove Interactive mixed method parsimony
fpars Discrete character parsimony
fpenny Penny algorithm, branch-and-bound
PHYLOGENY DISTANCE MATRIX
efitch Fitch-Margoliash and Least-Squares Distance Methods
ekitsch Fitch-Margoliash method with contemporary tips
eneighbor Phylogenies from distance matrix by N-J or UPGMA method
ffitch Fitch-Margoliash and Least-Squares Distance Methods
fkitsch Fitch-Margoliash method with contemporary tips
fneighbor Phylogenies from distance matrix by N-J or UPGMA method
PHYLOGENY GENE FREQUENCIES
egendist Genetic Distance Matrix program
fcontml Gene frequency and continuous character Maximum Likelihood
fgendist Compute genetic distances from gene frequencies
PHYLOGENY MOLECULAR SEQUENCE
distmat 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 Estimates nucleotide phylogeny by maximum likelihood
fdnamlk Estimates nucleotide phylogeny by maximum likelihood
fdnamove Interactive DNA parsimony
fdnapars DNA parsimony algorithm
fdnapenny Penny algorithm for DNA
fdolmove Interactive Dollo or Polymorphism Parsimony
ffreqboot Bootstrapped genetic frequencies algorithm
fproml Protein phylogeny by maximum likelihood
fpromlk Protein phylogeny by maximum likelihood
fprotdist Protein distance algorithm
fprotpars Protein parsimony algorithm
frestboot Bootstrapped restriction sites algorithm
frestdist Distance matrix from restriction sites or fragments
frestml Restriction site maximum Likelihood method
fseqboot Bootstrapped sequences algorithm
fseqbootall Bootstrapped sequences algorithm
PHYLOGENY TREE DRAWING
fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree Plots an unrooted tree diagram
fretree Interactive tree rearrangement
PROTEIN 2D STRUCTURE
garnier Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
pepcoil Predicts 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 Reports on protein proteolytic enzyme or reagent cleavage sites
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculates statistics of protein properties
wordcount Count and extract unique words in molecular sequence(s)
PROTEIN DOMAINS
cathparse Generates DCF file from raw CATH files
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainnr Removes redundant domains from a DCF file
domainrep Reorder DCF file to identify representative structures
domainseqs Adds 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 Predicts coiled coil regions in protein sequences
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
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqfraggle Removes fragment sequences from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generates DHF files from keyword search of UniProt
ssematch Search a DCF file for secondary structure matches
PROTEIN FUNCTIONAL SITES
echlorop Reports presence of chloroplast transit peptides
elipop Prediction of lipoproteins
esignalp Reports protein signal cleavage sites
etmhmm Reports transmembrane helices
sigcleave Reports on signal cleavage sites in a protein sequence
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search
tmap Predict and plot transmembrane segments in protein sequences
topo Draws an image of a transmembrane protein
PROTEIN MODIFICATIONS
enetnglyc Reports N-glycosylation sites in human proteins
enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphos Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
eprop Reports propeptide cleavage sites in proteins
esignalp Reports protein signal cleavage sites
eyinoyang Reports O-(beta)-GlcNAc attachment sites
PROTEIN MOTIFS
antigenic Finds antigenic sites in proteins
eiprscan Motif detection
elipop Prediction of lipoproteins
emast Motif detection
ememe Multiple EM for Motif Elicitation
ememetext Multiple EM for Motif Elicitation. Text file only
epestfind Finds 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 Searches 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 Scans protein sequence(s) with fingerprints from the PRINTS databas
e
sigcleave Reports on signal cleavage sites in a protein sequence
PROTEIN MUTATION
msbar Mutate a sequence
shuffleseq Shuffles 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 Generates a sparse protein signature from an alignment
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search
sigscanlig Searches 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 Calculates 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 Answers every drug discovery question about a sequence
UTILS
embossdata Find and retrieve EMBOSS data files
embossversion Reports 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 Generates DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
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
jaspextract Extract data from JASPAR
pdbparse Parses 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 Processes 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 Removes 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
Finds 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 Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
allversusall Sequence similarity data from all-versus-all comparison
antigenic Finds antigenic sites in proteins
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 Generates server cache file for DAS servers or for the DAS regi
stry
cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch Generates server cache file for EB-eye search domains
cai Calculate codon adaptation index
cathparse Generates DCF file from raw CATH files
chaos Draw a chaos game representation plot for a nucleotide sequence
charge Draw a protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
chips Calculates Nc codon usage statistic
cirdna Draws circular maps 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 Answers 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 Removes a section from a sequence
dan Calculates 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 Removes 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 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 Draw a threshold dotplot of two sequences
dotpath Draw a non-overlapping wordmatch dotplot of two sequences
dottup Displays 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 Reports 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 Finds inverted repeats in nucleotide sequences
eiprscan Motif detection
ekitsch Fitch-Margoliash method with contemporary tips
elipop Prediction of lipoproteins
emast Motif detection
embossdata Find and retrieve EMBOSS data files
embossversion Reports 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 Reports N-glycosylation sites in human proteins
enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian pr
oteins
enetphos Reports ser, thr and tyr phosphorylation sites in eukaryotic pr
oteins
entret Retrieves sequence entries from flatfile databases and files
eomega Multiple sequence alignment (ClustalO wrapper)
eomegapp Profile with profile (ClustalO wrapper)
eomegash Sequence with HMM (ClustalO wrapper)
eomegasp Sequence with profile (ClustalO wrapper)
epenny Penny algorithm, branch-and-bound
epestfind Finds PEST motifs as potential proteolytic cleavage sites
eprimer3 Picks PCR primers and hybridization oligos
eprimer32 Picks PCR primers and hybridization oligos
eprop Reports propeptide cleavage sites in proteins
eprotdist Protein distance algorithm
eprotpars Protein parsimony algorithm
equicktandem Finds tandem repeats in nucleotide sequences
erestml Restriction site Maximum Likelihood method
eseqboot Bootstrapped sequences algorithm
esignalp Reports protein signal cleavage sites
esim4 Align an mRNA to a genomic DNA sequence
est2genome Align EST sequences to genomic DNA sequence
etandem Finds 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 Reports 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 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
featcopy Reads and writes a feature table
featreport Reads and writes 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 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 Search for patterns in nucleotide sequences
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
garnier Predicts protein secondary structure using GOR method
geecee Calculate fractional GC content of nucleic acid sequences
getorf Finds and extracts 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 Converts 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
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 Plots isochores in DNA sequences
jaspextract Extract data from JASPAR
jaspscan Scans DNA sequences for transcription factors
libgen Generate discriminating elements from alignments
lindna Draws linear maps of DNA constructs
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein sequences
marscan Finds matrix/scaffold recognition (MRS) signatures in DNA seque
nces
maskambignuc Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks 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 Reads and writes (returns) 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 RNA alignment folding
ovrnaalifoldpf RNA alignment folding with partition
ovrnacofold RNA cofolding
ovrnacofoldconc RNA cofolding with concentrations
ovrnacofoldpf RNA cofolding with partitioning
ovrnadistance RNA distances
ovrnaduplex RNA duplex calculation
ovrnaeval RNA eval
ovrnaevalpair RNA eval with cofold
ovrnafold Calculate secondary structures of RNAs
ovrnafoldpf Secondary structures of RNAs with partition
ovrnaheat RNA melting
ovrnainverse RNA sequences matching a structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Plot vrnafold output
ovrnasubopt Calculate RNA suboptimals
palindrome Finds inverted repeats in nucleotide sequence(s)
pasteseq Insert one sequence into another
patmatdb Searches protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
pdbparse Parses 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 Predicts coiled coil regions in protein sequences
pepdigest Reports 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 Calculates 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 Processes the PROSITE motif database for use by patmatmotifs
pscan Scans protein sequence(s) with fingerprints from the PRINTS dat
abase
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
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 Generates a hits file from comparing two DHF files
rocplot Performs ROC analysis on hits files
scopparse Generate DCF file from raw SCOP files
seealso Finds programs with similar function to a specified program
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqcount Reads and counts sequences
seqfraggle Removes fragment sequences from DHF files
seqmatchall All-against-all word comparison of a sequence set
seqnr Removes redundancy from DHF files
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of sequences
seqretsplit Reads sequences and writes them to 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
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 Displays information on configured databases
showfeat Display features of a sequence in pretty format
showorf Display a nucleotide sequence and translation in pretty format
showpep Displays protein sequences with features in pretty format
showseq Displays sequences with features in pretty format
showserver Displays information on configured servers
shuffleseq Shuffles a set of sequences maintaining composition
sigcleave Reports on signal cleavage sites in a protein sequence
siggen Generates a sparse protein signature from an alignment
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search
sigscanlig Searches ligand-signature library and writes hits (LHF file)
silent Find restriction sites to insert (mutate) with no translation c
hange
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
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) 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 Displays full documentation for an application
tfscan Identify transcription factor binding sites in DNA sequences
tmap Predict and plot transmembrane segments in protein sequences
topo Draws 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 Finds neighbouring pairs of features in sequence(s)
union Concatenate multiple sequences into a single sequence
urlget Get URLs of data resources
vectorstrip Removes vectors from the ends of nucleotide sequence(s)
vrna2dfold Structures and samples of k,l neighbourhoods
vrnaaliduplex RNA duplex calculation for two sequence alignments
vrnaalifold RNA alignment folding
vrnaalifoldpf RNA alignment folding with partition
vrnacofold RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf RNA cofolding with partitioning
vrnadistance RNA distances
vrnaduplex RNA duplex calculation
vrnaeval RNA eval
vrnaevalpair RNA eval with cofold
vrnafold Calculate secondary structures of RNAs
vrnafoldpf Secondary structures of RNAs with partition
vrnaheat RNA melting
vrnainverse RNA sequences matching a structure
vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Locally stable secondary structures of RNAs plus zscore
vrnapkplex RNA structures plus pseudoknots
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals
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 Finds regions of identity (exact matches) of two sequences
wossdata Finds programs by EDAM data
wossinput Finds programs by EDAM input data
wossname Finds programs by keywords in their short description
wossoperation Finds programs by EDAM operation
wossoutput Finds programs by EDAM output data
wossparam Finds programs by EDAM parameter
wosstopic Finds programs by EDAM topic
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
Finds 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 TEXT DATA
DATA RETRIEVAL TOOL DATA
DATA RETRIEVAL URL 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
Finds programs by keywords in their short description
Go to the output files for this example
Command line arguments
Finds programs by keywords in their short description
Version: EMBOSS:6.4.0.0
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
ALIGNMENT
ALIGNMENT CONSENSUS
|
Command line arguments
Displays full documentation for an application
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-program] string Enter the name of an EMBOSS program (Any
string of at least 1 characters)
Additional (Optional) qualifiers:
-outfile outfile [stdout] Program documentation text output
file
-html boolean [N] This will format the output for
displaying as a WWW document.
-more boolean [@(!$(html))] This uses the standard UNIX
utility 'more' to display the text
page-by-page, waiting for you to read one
screen-full before going on to the next
page. When you have finished reading a page,
press the SPACE bar to proceed to the next
page.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-program] (Parameter 1) |
string | Enter the name of an EMBOSS program | Any string of at least 1 characters | Required |
| Additional (Optional) qualifiers | ||||
| -outfile | outfile | Program documentation text output file | Output file | stdout |
| -html | boolean | This will format the output for displaying as a WWW document. | Boolean value Yes/No | No |
| -more | boolean | This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page. | Boolean value Yes/No | @(!$(html)) |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
Input file format
None.
Output file format
Text documentation is output.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
The original data for the documentation can be found in: http://emboss.sourceforge.net/apps/ but please note that this is the documentation for the current development version. The documentation for your release should be nistalled somewhere on your system.Notes
The documentation for your own release is included as HTML pages in the EMBOSS distribution and may be available at your site. The same documentation is also available however through the program tfm as plain text. The documentation for all current and some past releases is provided by the developers at http://emboss.sourceforge.net/apps/. All EMBOSS programs should be adequately described. If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@emboss.open-bio.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 screentfm is unusual for an EMBOSS program in that it expects to be used interactively and so it displays the documentation text a page at a time, pausing after every page for the user to press the SPACE bar on their keyboard, i.e. it uses the UNIX program more to display the information. This behaviour can be turned off by using the qualifier -nomore.
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 with 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.
References
None.Warnings
None.Diagnostic Error Messages
tfm will warn you if you have supplied the name of a program which is not documented yet or which doesn't exist in EMBOSS.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| seealso | Finds programs with similar function to a specified program |
| wossdata | Finds programs by EDAM data |
| wossinput | Finds programs by EDAM input data |
| wossname | Finds programs by keywords in their short description |
| wossoperation | Finds programs by EDAM operation |
| wossoutput | Finds programs by EDAM output data |
| wossparam | Finds programs by EDAM parameter |
| wosstopic | Finds 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 © emboss.open-bio.org) not to the original author.