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