
                                 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

   <h2><a name="ACD">ACD</a></h2> <table border cellpadding=4
   bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr>
   <tr> <td><a href="acdc.html">acdc</a></td> <td>ACD compiler</td> </tr>
   <tr> <td><a href="acdpretty.html">acdpretty</a></td> <td>ACD pretty
   printing utility</td> </tr> <tr> <td><a
   href="acdtable.html">acdtable</a></td> <td>Creates an HTML table from
   an ACD file</td> </tr> <tr> <td><a
   href="acdtrace.html">acdtrace</a></td> <td>ACD compiler on-screen
   trace</td> </tr> <tr> <td><a href="acdvalid.html">acdvalid</a></td>
   <td>ACD file validation</td> </tr> </table> <h2><a name="ALIGNMENT
   CONSENSUS">ALIGNMENT CONSENSUS</a></h2> <table border cellpadding=4
   bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr>
   <tr> <td><a href="cons.html">cons</a></td> <td>Creates a consensus
   from multiple alignments</td> </tr> <tr> <td><a
   href="megamerger.html">megamerger</a></td> <td>Merge two large
   overlapping nucleic acid sequences</td> </tr> <tr> <td><a
   href="merger.html">merger</a></td> <td>Merge two overlapping
   sequences</td> </tr> </table> <h2><a name="ALIGNMENT
   DIFFERENCES">ALIGNMENT DIFFERENCES</a></h2> <table border
   cellpadding=4 bgcolor="#FFFFF0"> [Part of this file has been deleted
   for brevity] <tr><th>Program name</th><th>Description</th></tr> <tr>
   <td><a href="dbiblast.html">dbiblast</a></td> <td>Index a BLAST
   database</td> </tr> <tr> <td><a href="dbifasta.html">dbifasta</a></td>
   <td>Database indexing for fasta file databases</td> </tr> <tr> <td><a
   href="dbiflat.html">dbiflat</a></td> <td>Index a flat file
   database</td> </tr> <tr> <td><a href="dbigcg.html">dbigcg</a></td>
   <td>Index a GCG formatted database</td> </tr> <tr> <td><a
   href="dbxfasta.html">dbxfasta</a></td> <td>Database b+tree indexing
   for fasta file databases</td> </tr> <tr> <td><a
   href="dbxflat.html">dbxflat</a></td> <td>Database b+tree indexing for
   flat file databases</td> </tr> <tr> <td><a
   href="dbxgcg.html">dbxgcg</a></td> <td>Database b+tree indexing for
   GCG formatted databases</td> </tr> </table> <h2><a name="UTILS
   MISC">UTILS MISC</a></h2> <table border cellpadding=4
   bgcolor="#FFFFF0"> <tr><th>Program name</th><th>Description</th></tr>
   <tr> <td><a href="embossdata.html">embossdata</a></td> <td>Finds or
   fetches data files read by EMBOSS programs</td> </tr> <tr> <td><a
   href="embossversion.html">embossversion</a></td> <td>Writes the
   current EMBOSS version number</td> </tr> </table>

   If the -html, -prelink and -postlink qualifiers are specified, then
   the output will be wrapped in HTML tags, ready for inclusion in a Web
   page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are
   not output by this program as the list of programs is expected to form
   only part of the contents of a web page - the rest of the web page
   must be supplied by the user.

Data files

   As noted above, the program ACD files are searched. The average user
   will not need to worry about this.

Notes

   If a program's ACD file does not assign the program to a group, it
   will be automatically assigned to the group 'ASSORTED'.

   A program can belong to more than one group.

   The name of this program comes from its use as a favorite word of the
   author Terry Pratchett. It is used especially by the characters of the
   parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0

Known bugs

   None.

See also

   Program name                        Description
   infoalign    Information on a multiple sequence alignment
   infoseq      Displays some simple information about sequences
   seealso      Finds programs sharing group names
   showdb       Displays information on the currently available databases
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   tfm          Displays a program's help documentation manual
   whichdb      Search all databases for an entry

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
