tfm

 

Function

Displays full documentation for an application

Description

tfm displays help information for the specified EMBOSS program.

Usage

Here is a sample session with tfm


% tfm wossname 
Displays full documentation for an application

::::::::::::::
/homes/pmr/local/share/EMBOSS/doc/programs/text/wossname.txt
::::::::::::::

                                 wossname 



Function

   Finds programs by keywords in their short description

Description

   wossname search for the specified keywords (or parts thereof) in the
   application short description (as displayed by a program when it
   starts), functional group name and keywords. The group name,
   application name and short description of any matching applications is
   output (screen by default). If no search words are specified, then
   details of all the EMBOSS programs are output. There are various
   options for controlling how the search is performed and what is given
   in the output file. Optionally, the output will be wrapped in HTML
   tags ready for inclusion in a Web page.

Usage

   Here is a sample session with wossname

   Search for programs with 'restrict' in their description:


% wossname restrict 
Finds programs by keywords in their short description

SEARCH FOR 'RESTRICT'
erestml          Restriction site Maximum Likelihood method
frestboot        Bootstrapped restriction sites algorithm
frestdist        Distance matrix from restriction sites or fragments
frestml          Restriction site maximum Likelihood method
rebaseextract    Process the REBASE database for use by restriction enzyme appl
ications
recoder          Find restriction sites to remove (mutate) with no translation
change
redata           Retrieve information from REBASE restriction enzyme database
remap            Display restriction enzyme binding sites in a nucleotide seque
nce
restover         Find restriction enzymes producing a specific overhang
restrict         Report restriction enzyme cleavage sites in a nucleotide seque
nce
showseq          Displays sequences with features in pretty format
silent           Find restriction sites to insert (mutate) with no translation
change


   Example 2

   Display a listing of programs in their groups:


% wossname -search '' 
Finds programs by keywords in their short description

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

ALIGNMENT CONSENSUS
cons             Create a consensus sequence from a multiple alignment
consambig        Create an ambiguouos consensus sequence from a multiple alignm
ent
megamerger       Merge two large overlapping DNA sequences
merger           Merge two overlapping sequences

ALIGNMENT DIFFERENCES
diffseq          Compare and report features of two similar sequences

ALIGNMENT DOT PLOTS
dotmatcher       Draw a threshold dotplot of two sequences
dotpath          Draw a non-overlapping wordmatch dotplot of two sequences
dottup           Displays a wordmatch dotplot of two sequences
polydot          Draw dotplots for all-against-all comparison of a sequence set

ALIGNMENT GLOBAL
esim4            Align an mRNA to a genomic DNA sequence
est2genome       Align EST sequences to genomic DNA sequence
needle           Needleman-Wunsch global alignment of two sequences
stretcher        Needleman-Wunsch rapid global alignment of two sequences

ALIGNMENT LOCAL
matcher          Waterman-Eggert local alignment of two sequences
seqmatchall      All-against-all word comparison of a sequence set
supermatcher     Calculate approximate local pair-wise alignments of larger seq
uences
water            Smith-Waterman local alignment of sequences
wordfinder       Match large sequences against one or more other sequences
wordmatch        Finds regions of identity (exact matches) of two sequences

ALIGNMENT MULTIPLE
edialign         Local multiple alignment of sequences
emma             Multiple sequence alignment (ClustalW wrapper)
infoalign        Display basic information about a multiple sequence alignment
mse              Multiple Sequence Editor
plotcon          Plot conservation of a sequence alignment
prettyplot       Draw a sequence alignment with pretty formatting
showalign        Display a multiple sequence alignment in pretty format
tranalign        Generate an aligment of nucleic coding regions from aligned pr
oteins

ASSEMBLY FRAGMENT ASSEMBLY
emira            MIRA fragment assembly program
emiraest         MIRAest fragment assembly program

DISPLAY
abiview          Display the trace in an ABI sequencer file
cirdna           Draws circular maps of DNA constructs
lindna           Draws linear maps of DNA constructs
pepnet           Draw a helical net for a protein sequence
pepwheel         Draw a helical wheel diagram for a protein sequence
prettyplot       Draw a sequence alignment with pretty formatting
prettyseq        Write a nucleotide sequence and its translation to file
remap            Display restriction enzyme binding sites in a nucleotide seque
nce
seealso          Finds programs with similar function to a specified program
showalign        Display a multiple sequence alignment in pretty format
showdb           Displays information on configured databases
showfeat         Display features of a sequence in pretty format
showseq          Displays sequences with features in pretty format
sixpack          Display a DNA sequence with 6-frame translation and ORFs
textsearch       Search the textual description of sequence(s)

EDIT
aligncopy        Reads and writes alignments
aligncopypair    Reads and writes pairs from alignments
biosed           Replace or delete sequence sections
codcopy          Copy and reformat a codon usage table
cutseq           Removes a section from a sequence
degapseq         Removes non-alphabetic (e.g. gap) characters from sequences
descseq          Alter the name or description of a sequence
entret           Retrieves sequence entries from flatfile databases and files
extractalign     Extract regions from a sequence alignment
extractfeat      Extract features from sequence(s)
extractseq       Extract regions from a sequence
featcopy         Reads and writes a feature table
featreport       Reads and writes a feature table
listor           Write a list file of the logical OR of two sets of sequences
makenucseq       Create random nucleotide sequences
makeprotseq      Create random protein sequences
maskambignuc     Masks all ambiguity characters in nucleotide sequences with N
maskambigprot    Masks all ambiguity characters in protein sequences with X
maskfeat         Write a sequence with masked features
maskseq          Write a sequence with masked regions
newseq           Create a sequence file from a typed-in sequence
nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn         Remove carriage return from ASCII files
nospace          Remove all whitespace from an ASCII text file
notab            Replace tabs with spaces in an ASCII text file
notseq           Write to file a subset of an input stream of sequences
nthseq           Write to file a single sequence from an input stream of sequen
ces
pasteseq         Insert one sequence into another
revseq           Reverse and complement a nucleotide sequence
seqret           Reads and writes (returns) sequences
seqretsplit      Reads sequences and writes them to individual files
sizeseq          Sort sequences by size
skipredundant    Remove redundant sequences from an input set
skipseq          Reads and writes (returns) sequences, skipping first few
splitter         Split sequence(s) into smaller sequences
trimest          Remove poly-A tails from nucleotide sequences
trimseq          Remove unwanted characters from start and end of sequence(s)
trimspace        Remove extra whitespace from an ASCII text file
union            Concatenate multiple sequences into a single sequence
vectorstrip      Removes vectors from the ends of nucleotide sequence(s)
yank             Add a sequence reference (a full USA) to a list file

ENZYME KINETICS
findkm           Calculate and plot enzyme reaction data

FEATURE TABLES
coderet          Extract CDS, mRNA and translations from feature tables
extractfeat      Extract features from sequence(s)
maskfeat         Write a sequence with masked features
showfeat         Display features of a sequence in pretty format
twofeat          Finds neighbouring pairs of features in sequence(s)

HMM
ehmmalign        Align sequences to an HMM profile
ehmmbuild        Build a profile HMM from an alignment
ehmmcalibrate    Calibrate HMM search statistics
ehmmconvert      Convert between profile HMM file formats
ehmmemit         Generate sequences from a profile HMM
ehmmfetch        Retrieve an HMM from an HMM database
ehmmindex        Create a binary SSI index for an HMM database
ehmmpfam         Search one or more sequences against an HMM database
ehmmsearch       Search a sequence database with a profile HMM
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        Display basic information about a multiple sequence alignment
infobase         Return information on a given nucleotide base
inforesidue      Return information on a given amino acid residue
infoseq          Display basic information about sequences
seealso          Finds programs with similar function to a specified program
showdb           Displays information on configured databases
textsearch       Search the textual description of sequence(s)
tfm              Displays full documentation for an application
whichdb          Search all sequence databases for an entry and retrieve it
wossname         Finds programs by keywords in their short description

MENUS
emnu             Simple menu of EMBOSS applications

NUCLEIC 2D STRUCTURE
einverted        Finds inverted repeats in nucleotide 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

NUCLEIC CODON USAGE
cai              Calculate codon adaptation index
chips            Calculates Nc codon usage statistic
codcmp           Codon usage table comparison
cusp             Create a codon usage table from nucleotide sequence(s)
syco             Draw synonymous codon usage statictic plot for a nucleotide se
quence

NUCLEIC COMPOSITION
banana           Plot bending and curvature data for B-DNA
btwisted         Calculate the twisting in a B-DNA sequence
chaos            Draw a chaos game representation plot for a nucleotide sequenc
e
compseq          Calculate the composition of unique words in sequences
dan              Calculates nucleic acid melting temperature
density          Draw a nucleic acid density plot
freak            Generate residue/base frequency table or plot
isochore         Plots isochores in DNA sequences
sirna            Finds siRNA duplexes in mRNA
wordcount        Count and extract unique words in DNA sequence(s)

NUCLEIC CPG ISLANDS
cpgplot          Identify and plot CpG islands in nucleotide sequence(s)
cpgreport        Identify and report CpG-rich regions in nucleotide sequence(s)
geecee           Calculate fractional GC content of nucleic acid sequences
newcpgreport     Identify CpG islands in nucleotide sequence(s)
newcpgseek       Identify and report CpG-rich regions in nucleotide sequence(s)

NUCLEIC GENE FINDING
getorf           Finds and extracts open reading frames (ORFs)
marscan          Finds matrix/scaffold recognition (MRS) signatures in DNA sequ
ences
plotorf          Plot potential open reading frames in a nucleotide sequence
showorf          Display a nucleotide sequence and translation in pretty format
sixpack          Display a DNA sequence with 6-frame translation and ORFs
syco             Draw synonymous codon usage statictic plot for a nucleotide se
quence
tcode            Identify protein-coding regions using Fickett TESTCODE statist
ic
wobble           Plot third base position variability in a nucleotide sequence

NUCLEIC MOTIFS
dreg             Regular expression search of nucleotide sequence(s)
fuzznuc          Search for patterns in nucleotide sequences
fuzztran         Search for patterns in protein sequences (translated)
marscan          Finds matrix/scaffold recognition (MRS) signatures in DNA sequ
ences

NUCLEIC MUTATION
msbar            Mutate a sequence
shuffleseq       Shuffles a set of sequences maintaining composition

NUCLEIC PRIMERS
eprimer3         Picks PCR primers and hybridization oligos
primersearch     Search DNA sequences for matches with primer pairs
stssearch        Search a DNA database for matches with a set of STS primers

NUCLEIC PROFILES
profit           Scan one or more sequences with a simple frequency matrix
prophecy         Create frequency matrix or profile from a multiple alignment
prophet          Scan one or more sequences with a Gribskov or Henikoff profile

NUCLEIC REPEATS
einverted        Finds inverted repeats in nucleotide sequences
equicktandem     Finds tandem repeats in nucleotide sequences
etandem          Finds tandem repeats in a nucleotide sequence
palindrome       Finds inverted repeats in nucleotide sequence(s)

NUCLEIC RESTRICTION
recoder          Find restriction sites to remove (mutate) with no translation
change
redata           Retrieve information from REBASE restriction enzyme database
remap            Display restriction enzyme binding sites in a nucleotide seque
nce
restover         Find restriction enzymes producing a specific overhang
restrict         Report restriction enzyme cleavage sites in a nucleotide seque
nce
showseq          Displays sequences with features in pretty format
silent           Find restriction sites to insert (mutate) with no translation
change

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
jaspscan         Scans DNA sequences for transcription factors
tfscan           Identify transcription factor binding sites in DNA sequences

NUCLEIC TRANSLATION
backtranambig    Back-translate a protein sequence to ambiguous nucleotide sequ
ence
backtranseq      Back-translate a protein sequence to a nucleotide sequence
coderet          Extract CDS, mRNA and translations from feature tables
plotorf          Plot potential open reading frames in a nucleotide sequence
prettyseq        Write a nucleotide sequence and its translation to file
remap            Display restriction enzyme binding sites in a nucleotide seque
nce
showorf          Display a nucleotide sequence and translation in pretty format
showseq          Displays sequences with features in pretty format
sixpack          Display a DNA sequence with 6-frame translation and ORFs
transeq          Translate nucleic acid sequences

PHYLOGENY CONSENSUS
econsense        Majority-rule and strict consensus tree
fconsense        Majority-rule and strict consensus tree
ftreedist        Distances between trees
ftreedistpair    Distances between two sets of trees

PHYLOGENY CONTINUOUS CHARACTERS
econtml          Continuous character Maximum Likelihood method
econtrast        Continuous character Contrasts
fcontrast        Continuous character Contrasts

PHYLOGENY DISCRETE CHARACTERS
eclique          Largest clique program
edollop          Dollo and polymorphism parsimony algorithm
edolpenny        Penny algorithm Dollo or polymorphism
efactor          Multistate to binary recoding program
emix             Mixed parsimony algorithm
epenny           Penny algorithm, branch-and-bound
fclique          Largest clique program
fdollop          Dollo and polymorphism parsimony algorithm
fdolpenny        Penny algorithm Dollo or polymorphism
ffactor          Multistate to binary recoding program
fmix             Mixed parsimony algorithm
fmove            Interactive mixed method parsimony
fpars            Discrete character parsimony
fpenny           Penny algorithm, branch-and-bound

PHYLOGENY DISTANCE MATRIX
efitch           Fitch-Margoliash and Least-Squares Distance Methods
ekitsch          Fitch-Margoliash method with contemporary tips
eneighbor        Phylogenies from distance matrix by N-J or UPGMA method
ffitch           Fitch-Margoliash and Least-Squares Distance Methods
fkitsch          Fitch-Margoliash method with contemporary tips
fneighbor        Phylogenies from distance matrix by N-J or UPGMA method

PHYLOGENY GENE FREQUENCIES
egendist         Genetic Distance Matrix program
fcontml          Gene frequency and continuous character Maximum Likelihood
fgendist         Compute genetic distances from gene frequencies

PHYLOGENY MOLECULAR SEQUENCE
distmat          Create a distance matrix from a multiple sequence alignment
ednacomp         DNA compatibility algorithm
ednadist         Nucleic acid sequence Distance Matrix program
ednainvar        Nucleic acid sequence Invariants method
ednaml           Phylogenies from nucleic acid Maximum Likelihood
ednamlk          Phylogenies from nucleic acid Maximum Likelihood with clock
ednapars         DNA parsimony algorithm
ednapenny        Penny algorithm for DNA
eprotdist        Protein distance algorithm
eprotpars        Protein parsimony algorithm
erestml          Restriction site Maximum Likelihood method
eseqboot         Bootstrapped sequences algorithm
fdiscboot        Bootstrapped discrete sites algorithm
fdnacomp         DNA compatibility algorithm
fdnadist         Nucleic acid sequence Distance Matrix program
fdnainvar        Nucleic acid sequence Invariants method
fdnaml           Estimates nucleotide phylogeny by maximum likelihood
fdnamlk          Estimates nucleotide phylogeny by maximum likelihood
fdnamove         Interactive DNA parsimony
fdnapars         DNA parsimony algorithm
fdnapenny        Penny algorithm for DNA
fdolmove         Interactive Dollo or Polymorphism Parsimony
ffreqboot        Bootstrapped genetic frequencies algorithm
fproml           Protein phylogeny by maximum likelihood
fpromlk          Protein phylogeny by maximum likelihood
fprotdist        Protein distance algorithm
fprotpars        Protein parsimony algorithm
frestboot        Bootstrapped restriction sites algorithm
frestdist        Distance matrix from restriction sites or fragments
frestml          Restriction site maximum Likelihood method
fseqboot         Bootstrapped sequences algorithm
fseqbootall      Bootstrapped sequences algorithm

PHYLOGENY TREE DRAWING
fdrawgram        Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree        Plots an unrooted tree diagram
fretree          Interactive tree rearrangement

PROTEIN 2D STRUCTURE
garnier          Predicts protein secondary structure using GOR method
helixturnhelix   Identify nucleic acid-binding motifs in protein sequences
hmoment          Calculate and plot hydrophobic moment for protein sequence(s)
pepcoil          Predicts coiled coil regions in protein sequences
pepnet           Draw a helical net for a protein sequence
pepwheel         Draw a helical wheel diagram for a protein sequence
tmap             Predict and plot transmembrane segments in protein sequences
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           Calculates 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 nucleotide sequ
ence
backtranseq      Back-translate a protein sequence to a nucleotide sequence
charge           Draw a protein charge plot
checktrans       Reports STOP codons and ORF statistics of a protein
compseq          Calculate the composition of unique words in sequences
emowse           Search protein sequences by digest fragment molecular weight
freak            Generate residue/base frequency table or plot
iep              Calculate the isoelectric point of proteins
mwcontam         Find weights common to multiple molecular weights files
mwfilter         Filter noisy data from molecular weights file
octanol          Draw a White-Wimley protein hydropathy plot
pepinfo          Plot amino acid properties of a protein sequence in parallel
pepstats         Calculates statistics of protein properties
pepwindow        Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount        Count and extract unique words in DNA sequence(s)

PROTEIN MOTIFS
antigenic        Finds antigenic sites in proteins
digest           Reports on protein proteolytic enzyme or reagent cleavage site
s
echlorop         Reports presence of chloroplast transit peptides
eiprscan         Motif detection
elipop           Prediction of lipoproteins
emast            Motif detection
ememe            Motif detection
enetnglyc        Reports N-glycosylation sites in human proteins
enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian p
roteins
enetphos         Reports ser, thr and tyr phosphorylation sites in eukaryotic p
roteins
epestfind        Finds PEST motifs as potential proteolytic cleavage sites
eprop            Reports propeptide cleavage sites in proteins
esignalp         Reports protein signal cleavage sites
etmhmm           Reports transmembrane helices
eyinoyang        Reports O-(beta)-GlcNAc attachment sites
fuzzpro          Search for patterns in protein sequences
fuzztran         Search for patterns in protein sequences (translated)
helixturnhelix   Identify nucleic acid-binding motifs in protein sequences
oddcomp          Identify proteins with specified sequence word composition
omeme            Motif detection
patmatdb         Searches protein sequences with a sequence motif
patmatmotifs     Scan a protein sequence with motifs from the PROSITE database
pepcoil          Predicts coiled coil regions in protein sequences
preg             Regular expression search of protein sequence(s)
pscan            Scans protein sequence(s) with fingerprints from the PRINTS da
tabase
sigcleave        Reports on signal cleavage sites in a protein sequence

PROTEIN MUTATION
msbar            Mutate a sequence
shuffleseq       Shuffles a set of sequences maintaining composition

PROTEIN PROFILES
profit           Scan one or more sequences with a simple frequency matrix
prophecy         Create frequency matrix or profile from a multiple alignment
prophet          Scan one or more sequences with a Gribskov or Henikoff profile

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 amino acid property data from AAINDEX
allversusall     Sequence similarity data from all-versus-all comparison
cathparse        Generates DCF file from raw CATH files
cutgextract      Extract codon usage tables from from CUTG database
domainer         Generates domain CCF files from protein CCF files
domainnr         Removes redundant domains from a DCF file
domainseqs       Adds sequence records to a DCF file
domainsse        Add secondary structure records to a DCF file
hetparse         Converts heterogen group dictionary to EMBL-like format
jaspextract      Extract data from JASPAR
pdbparse         Parses PDB files and writes protein CCF files
pdbplus          Add accessibility & secondary structure to a CCF file
pdbtosp          Convert swissprot:PDB codes file to EMBL-like format
printsextract    Extract data from PRINTS database for use by pscan
prosextract      Processes the PROSITE motif database for use by patmatmotifs
rebaseextract    Process the REBASE database for use by restriction enzyme appl
ications
scopparse        Generate DCF file from raw SCOP files
seqnr            Removes redundancy from DHF files
sites            Generate residue-ligand CON files from CCF files
ssematch         Search a DCF file for secondary structure matches
tfextract        Process TRANSFAC transcription factor database for use by tfsc
an

UTILS DATABASE INDEXING
dbiblast         Index a BLAST database
dbifasta         Index a fasta file database
dbiflat          Index a flat file database
dbigcg           Index a GCG formatted database
dbxfasta         Index a fasta file database using b+tree indices
dbxflat          Index a flat file database using b+tree indices
dbxgcg           Index a GCG formatted database using b+tree indices

UTILS MISC
embossdata       Find and retrieve EMBOSS data files
embossversion    Writes the current EMBOSS version number to a file


   Example 3

   Display an alphabetic listing of all programs:


% wossname -search '' -alphabetic 
Finds programs by keywords in their short description

ALPHABETIC LIST OF PROGRAMS
aaindexextract   Extract amino acid property data from AAINDEX
abiview          Display the trace in an ABI sequencer file
acdc             Test an application ACD file
acdpretty        Correctly reformat an application ACD file
acdtable         Generate an HTML table of parameters from an application ACD f
ile
acdtrace         Trace processing of an application ACD file (for testing)
acdvalid         Validate an application ACD file
aligncopy        Reads and writes alignments
aligncopypair    Reads and writes pairs from alignments
allversusall     Sequence similarity data from all-versus-all comparison
antigenic        Finds antigenic sites in proteins
backtranambig    Back-translate a protein sequence to ambiguous nucleotide sequ
ence
backtranseq      Back-translate a protein sequence to a nucleotide sequence
banana           Plot bending and curvature data for B-DNA
biosed           Replace or delete sequence sections
btwisted         Calculate the twisting in a B-DNA sequence
cai              Calculate codon adaptation index
cathparse        Generates DCF file from raw CATH files
chaos            Draw a chaos game representation plot for a nucleotide sequenc
e
charge           Draw a protein charge plot
checktrans       Reports STOP codons and ORF statistics of a protein
chips            Calculates Nc codon usage statistic
cirdna           Draws circular maps of DNA constructs
codcmp           Codon usage table comparison
codcopy          Copy and reformat a codon usage table
coderet          Extract CDS, mRNA and translations from feature tables
compseq          Calculate the composition of unique words in sequences
cons             Create a consensus sequence from a multiple alignment
consambig        Create an ambiguouos consensus sequence from a multiple alignm
ent
contacts         Generate intra-chain CON files from CCF files
cpgplot          Identify and plot CpG islands in nucleotide sequence(s)
cpgreport        Identify and report CpG-rich regions in nucleotide sequence(s)
crystalball      Answers every drug discovery question about a sequence
cusp             Create a codon usage table from nucleotide sequence(s)
cutgextract      Extract codon usage tables from from CUTG database
cutseq           Removes a section from a sequence
dan              Calculates nucleic acid melting temperature
dbiblast         Index a BLAST database
dbifasta         Index a fasta file database
dbiflat          Index a flat file database
dbigcg           Index a GCG formatted database
dbxfasta         Index a fasta file database using b+tree indices
dbxflat          Index a flat file database using b+tree indices
dbxgcg           Index a GCG formatted database using b+tree indices
degapseq         Removes non-alphabetic (e.g. gap) characters from sequences
density          Draw a nucleic acid density plot
descseq          Alter the name or description of a sequence
diffseq          Compare and report features of two similar sequences
digest           Reports on protein proteolytic enzyme or reagent cleavage site
s
distmat          Create a distance matrix from a multiple sequence alignment
domainalign      Generate alignments (DAF file) for nodes in a DCF file
domainer         Generates domain CCF files from protein CCF files
domainnr         Removes redundant domains from a DCF file
domainrep        Reorder DCF file to identify representative structures
domainreso       Remove low resolution domains from a DCF file
domainseqs       Adds sequence records to a DCF file
domainsse        Add secondary structure records to a DCF file
dotmatcher       Draw a threshold dotplot of two sequences
dotpath          Draw a non-overlapping wordmatch dotplot of two sequences
dottup           Displays a wordmatch dotplot of two sequences
dreg             Regular expression search of nucleotide sequence(s)
echlorop         Reports presence of chloroplast transit peptides
eclique          Largest clique program
econsense        Majority-rule and strict consensus tree
econtml          Continuous character Maximum Likelihood method
econtrast        Continuous character Contrasts
edialign         Local multiple alignment of sequences
ednacomp         DNA compatibility algorithm
ednadist         Nucleic acid sequence Distance Matrix program
ednainvar        Nucleic acid sequence Invariants method
ednaml           Phylogenies from nucleic acid Maximum Likelihood
ednamlk          Phylogenies from nucleic acid Maximum Likelihood with clock
ednapars         DNA parsimony algorithm
ednapenny        Penny algorithm for DNA
edollop          Dollo and polymorphism parsimony algorithm
edolpenny        Penny algorithm Dollo or polymorphism
efactor          Multistate to binary recoding program
efitch           Fitch-Margoliash and Least-Squares Distance Methods
egendist         Genetic Distance Matrix program
ehmmalign        Align sequences to an HMM profile
ehmmbuild        Build a profile HMM from an alignment
ehmmcalibrate    Calibrate HMM search statistics
ehmmconvert      Convert between profile HMM file formats
ehmmemit         Generate sequences from a profile HMM
ehmmfetch        Retrieve an HMM from an HMM database
ehmmindex        Create a binary SSI index for an HMM database
ehmmpfam         Search one or more sequences against an HMM database
ehmmsearch       Search a sequence database with a profile HMM
einverted        Finds inverted repeats in nucleotide sequences
eiprscan         Motif detection
ekitsch          Fitch-Margoliash method with contemporary tips
elipop           Prediction of lipoproteins
emast            Motif detection
embossdata       Find and retrieve EMBOSS data files
embossversion    Writes the current EMBOSS version number to a file
ememe            Motif detection
emira            MIRA fragment assembly program
emiraest         MIRAest fragment assembly program
emix             Mixed parsimony algorithm
emma             Multiple sequence alignment (ClustalW wrapper)
emnu             Simple menu of EMBOSS applications
emowse           Search protein sequences by digest fragment molecular weight
eneighbor        Phylogenies from distance matrix by N-J or UPGMA method
enetnglyc        Reports N-glycosylation sites in human proteins
enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian p
roteins
enetphos         Reports ser, thr and tyr phosphorylation sites in eukaryotic p
roteins
entret           Retrieves sequence entries from flatfile databases and files
epenny           Penny algorithm, branch-and-bound
epestfind        Finds PEST motifs as potential proteolytic cleavage sites
eprimer3         Picks PCR primers and hybridization oligos
eprop            Reports propeptide cleavage sites in proteins
eprotdist        Protein distance algorithm
eprotpars        Protein parsimony algorithm
equicktandem     Finds tandem repeats in nucleotide sequences
erestml          Restriction site Maximum Likelihood method
eseqboot         Bootstrapped sequences algorithm
esignalp         Reports protein signal cleavage sites
esim4            Align an mRNA to a genomic DNA sequence
est2genome       Align EST sequences to genomic DNA sequence
etandem          Finds tandem repeats in a nucleotide sequence
etmhmm           Reports transmembrane helices
extractalign     Extract regions from a sequence alignment
extractfeat      Extract features from sequence(s)
extractseq       Extract regions from a sequence
eyinoyang        Reports O-(beta)-GlcNAc attachment sites
fclique          Largest clique program
fconsense        Majority-rule and strict consensus tree
fcontml          Gene frequency and continuous character Maximum Likelihood
fcontrast        Continuous character Contrasts
fdiscboot        Bootstrapped discrete sites algorithm
fdnacomp         DNA compatibility algorithm
fdnadist         Nucleic acid sequence Distance Matrix program
fdnainvar        Nucleic acid sequence Invariants method
fdnaml           Estimates nucleotide phylogeny by maximum likelihood
fdnamlk          Estimates nucleotide phylogeny by maximum likelihood
fdnamove         Interactive DNA parsimony
fdnapars         DNA parsimony algorithm
fdnapenny        Penny algorithm for DNA
fdollop          Dollo and polymorphism parsimony algorithm
fdolmove         Interactive Dollo or Polymorphism Parsimony
fdolpenny        Penny algorithm Dollo or polymorphism
fdrawgram        Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree        Plots an unrooted tree diagram
featcopy         Reads and writes a feature table
featreport       Reads and writes a feature table
ffactor          Multistate to binary recoding program
ffitch           Fitch-Margoliash and Least-Squares Distance Methods
ffreqboot        Bootstrapped genetic frequencies algorithm
fgendist         Compute genetic distances from gene frequencies
findkm           Calculate and plot enzyme reaction data
fkitsch          Fitch-Margoliash method with contemporary tips
fmix             Mixed parsimony algorithm
fmove            Interactive mixed method parsimony
fneighbor        Phylogenies from distance matrix by N-J or UPGMA method
fpars            Discrete character parsimony
fpenny           Penny algorithm, branch-and-bound
fproml           Protein phylogeny by maximum likelihood
fpromlk          Protein phylogeny by maximum likelihood
fprotdist        Protein distance algorithm
fprotpars        Protein parsimony algorithm
freak            Generate residue/base frequency table or plot
frestboot        Bootstrapped restriction sites algorithm
frestdist        Distance matrix from restriction sites or fragments
frestml          Restriction site maximum Likelihood method
fretree          Interactive tree rearrangement
fseqboot         Bootstrapped sequences algorithm
fseqbootall      Bootstrapped sequences algorithm
ftreedist        Distances between trees
ftreedistpair    Distances between two sets of trees
fuzznuc          Search for patterns in nucleotide sequences
fuzzpro          Search for patterns in protein sequences
fuzztran         Search for patterns in protein sequences (translated)
garnier          Predicts protein secondary structure using GOR method
geecee           Calculate fractional GC content of nucleic acid sequences
getorf           Finds and extracts open reading frames (ORFs)
helixturnhelix   Identify nucleic acid-binding motifs in protein sequences
hetparse         Converts heterogen group dictionary to EMBL-like format
hmoment          Calculate and plot hydrophobic moment for protein sequence(s)
iep              Calculate the isoelectric point of proteins
infoalign        Display basic information about a multiple sequence alignment
infobase         Return information on a given nucleotide base
inforesidue      Return information on a given amino acid residue
infoseq          Display basic information about sequences
interface        Generate inter-chain CON files from CCF files
isochore         Plots isochores in DNA sequences
jaspextract      Extract data from JASPAR
jaspscan         Scans DNA sequences for transcription factors
libgen           Generate discriminating elements from alignments
lindna           Draws linear maps of DNA constructs
listor           Write a list file of the logical OR of two sets of sequences
makenucseq       Create random nucleotide sequences
makeprotseq      Create random protein sequences
marscan          Finds matrix/scaffold recognition (MRS) signatures in DNA sequ
ences
maskambignuc     Masks all ambiguity characters in nucleotide sequences with N
maskambigprot    Masks all ambiguity characters in protein sequences with X
maskfeat         Write a sequence with masked features
maskseq          Write a sequence with masked regions
matcher          Waterman-Eggert local alignment of two sequences
matgen3d         Generate a 3D-1D scoring matrix from CCF files
megamerger       Merge two large overlapping DNA sequences
merger           Merge two overlapping sequences
msbar            Mutate a sequence
mse              Multiple Sequence Editor
mwcontam         Find weights common to multiple molecular weights files
mwfilter         Filter noisy data from molecular weights file
myseq            Demonstration of sequence reading
mytest           Demonstration of sequence reading
needle           Needleman-Wunsch global alignment of two sequences
newcpgreport     Identify CpG islands in nucleotide sequence(s)
newcpgseek       Identify and report CpG-rich regions in nucleotide sequence(s)
newseq           Create a sequence file from a typed-in sequence
nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn         Remove carriage return from ASCII files
nospace          Remove all whitespace from an ASCII text file
notab            Replace tabs with spaces in an ASCII text file
notseq           Write to file a subset of an input stream of sequences
nthseq           Write to file a single sequence from an input stream of sequen
ces
oalistat         Statistics for multiple alignment files
octanol          Draw a White-Wimley protein hydropathy plot
oddcomp          Identify proteins with specified sequence word composition
ohmmalign        Align sequences with an HMM
ohmmbuild        Build HMM
ohmmcalibrate    Calibrate a hidden Markov model
ohmmconvert      Convert between HMM formats
ohmmemit         Extract HMM sequences
ohmmfetch        Extract HMM from a database
ohmmindex        Index an HMM database
ohmmpfam         Align single sequence with an HMM
ohmmsearch       Search sequence database with an HMM
omeme            Motif detection
palindrome       Finds inverted repeats in nucleotide sequence(s)
pasteseq         Insert one sequence into another
patmatdb         Searches protein sequences with a sequence motif
patmatmotifs     Scan a protein sequence with motifs from the PROSITE database
pdbparse         Parses PDB files and writes protein CCF files
pdbplus          Add accessibility & secondary structure to a CCF file
pdbtosp          Convert swissprot:PDB codes file to EMBL-like format
pepcoil          Predicts coiled coil regions in protein sequences
pepinfo          Plot amino acid properties of a protein sequence in parallel
pepnet           Draw a helical net for a protein sequence
pepstats         Calculates statistics of protein properties
pepwheel         Draw a helical wheel diagram for a protein sequence
pepwindow        Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein alignment
plotcon          Plot conservation of a sequence alignment
plotorf          Plot potential open reading frames in a nucleotide sequence
polydot          Draw dotplots for all-against-all comparison of a sequence set
preg             Regular expression search of protein sequence(s)
prettyplot       Draw a sequence alignment with pretty formatting
prettyseq        Write a nucleotide sequence and its translation to file
primersearch     Search DNA sequences for matches with primer pairs
printsextract    Extract data from PRINTS database for use by pscan
profit           Scan one or more sequences with a simple frequency matrix
prophecy         Create frequency matrix or profile from a multiple alignment
prophet          Scan one or more sequences with a Gribskov or Henikoff profile
prosextract      Processes the PROSITE motif database for use by patmatmotifs
pscan            Scans protein sequence(s) with fingerprints from the PRINTS da
tabase
psiphi           Calculates phi and psi torsion angles from protein coordinates
rebaseextract    Process the REBASE database for use by restriction enzyme appl
ications
recoder          Find restriction sites to remove (mutate) with no translation
change
redata           Retrieve information from REBASE restriction enzyme database
remap            Display restriction enzyme binding sites in a nucleotide seque
nce
restover         Find restriction enzymes producing a specific overhang
restrict         Report restriction enzyme cleavage sites in a nucleotide seque
nce
revseq           Reverse and complement a nucleotide sequence
rocon            Generates a hits file from comparing two DHF files
rocplot          Performs ROC analysis on hits files
scopparse        Generate DCF file from raw SCOP files
seealso          Finds programs with similar function to a specified program
seqalign         Extend alignments (DAF file) with sequences (DHF file)
seqfraggle       Removes fragment sequences from DHF files
seqmatchall      All-against-all word comparison of a sequence set
seqnr            Removes redundancy from DHF files
seqret           Reads and writes (returns) sequences
seqretsplit      Reads sequences and writes them to individual files
seqsearch        Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort          Remove ambiguous classified sequences from DHF files
seqwords         Generates DHF files from keyword search of UniProt
showalign        Display a multiple sequence alignment in pretty format
showdb           Displays information on configured databases
showfeat         Display features of a sequence in pretty format
showorf          Display a nucleotide sequence and translation in pretty format
showseq          Displays sequences with features in pretty format
shuffleseq       Shuffles a set of sequences maintaining composition
sigcleave        Reports on signal cleavage sites in a protein sequence
siggen           Generates a sparse protein signature from an alignment
siggenlig        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           Find restriction sites to insert (mutate) with no translation
change
sirna            Finds siRNA duplexes in mRNA
sites            Generate residue-ligand CON files from CCF files
sixpack          Display a DNA sequence with 6-frame translation and ORFs
sizeseq          Sort sequences by size
skipredundant    Remove redundant sequences from an input set
skipseq          Reads and writes (returns) sequences, skipping first few
splitter         Split sequence(s) into smaller sequences
ssematch         Search a DCF file for secondary structure matches
stretcher        Needleman-Wunsch rapid global alignment of two sequences
stssearch        Search a DNA database for matches with a set of STS primers
supermatcher     Calculate approximate local pair-wise alignments of larger seq
uences
syco             Draw synonymous codon usage statictic plot for a nucleotide se
quence
tcode            Identify protein-coding regions using Fickett TESTCODE statist
ic
textsearch       Search the textual description of sequence(s)
tfextract        Process TRANSFAC transcription factor database for use by tfsc
an
tfm              Displays full documentation for an application
tfscan           Identify transcription factor binding sites in DNA sequences
tmap             Predict and plot transmembrane segments in protein sequences
topo             Draws an image of a transmembrane protein
tranalign        Generate an aligment of nucleic coding regions from aligned pr
oteins
transeq          Translate nucleic acid sequences
trimest          Remove poly-A tails from nucleotide sequences
trimseq          Remove unwanted characters from start and end of sequence(s)
trimspace        Remove extra whitespace from an ASCII text file
twofeat          Finds neighbouring pairs of features in sequence(s)
union            Concatenate multiple sequences into a single sequence
vectorstrip      Removes vectors from the ends of nucleotide sequence(s)
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 of sequences
whichdb          Search all sequence databases for an entry and retrieve it
wobble           Plot third base position variability in a nucleotide sequence
wordcount        Count and extract unique words in DNA sequence(s)
wordfinder       Match large sequences against one or more other sequences
wordmatch        Finds regions of identity (exact matches) of two sequences
wossname         Finds programs by keywords in their short description
yank             Add a sequence reference (a full USA) to a list file


   Example 4

   Display only the groups that the programs can belong to:


% wossname -search '' -groups 
Finds programs by keywords in their short description

ACD
ALIGNMENT CONSENSUS
ALIGNMENT DIFFERENCES
ALIGNMENT DOT PLOTS
ALIGNMENT GLOBAL
ALIGNMENT LOCAL
ALIGNMENT MULTIPLE
ASSEMBLY FRAGMENT ASSEMBLY
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 short description

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. 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

   

ACD

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

ALIGNMENT CONSENSUS

[Part of this file has been deleted for brevity]
Program name Description
cons Create a consensus sequence from a multiple alignment
consambig Create an ambiguouos consensus sequence from a multiple alignment
megamerger Merge two large overlapping DNA sequences
dbiblast Index a BLAST database
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
dbxfasta Index a fasta file database using b+tree indices
dbxflat Index a flat file database using b+tree indices
dbxgcg Index a GCG formatted database using b+tree indices

UTILS MISC

Program name Description
embossdata Find and retrieve EMBOSS data files
embossversion Writes the current EMBOSS version number to a file
If the -html, -prelink and -postlink qualifiers are specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as , , and are not output by this program as the list of programs is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user. Data files As noted above, the program ACD files are searched. The average user will not need to worry about this. Notes wossname reads the short descriptions and the program groups from the program ACD files. These file describe the command-line interface of the applications. You don't need to know about them unless you are writing EMBOSS programs. They are described in the EMBOSS Developers Manual. If a program's ACD file does not specify a program group, then it will be automatically assigned to the group ASSORTED in the output file. A program can belong to more than one group. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0 Known bugs None. See also Program name Description infoalign Display basic information about a multiple sequence alignment infobase Return information on a given nucleotide base inforesidue Return information on a given amino acid residue infoseq Display basic information about sequences seealso Finds programs with similar function to a specified program showdb Displays information on configured databases textsearch Search the textual description of sequence(s) tfm Displays full documentation for an application whichdb Search all sequence databases for an entry and retrieve it Author(s) Gary Williams (gwilliam rfcgr.mrc.ac.uk) MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None

Command line arguments

   Standard (Mandatory) qualifiers:
  [-program]           string     Enter the name of an EMBOSS program (Any
                                  string of at least 1 characters)

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

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. 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)

Input file format

None.

Output file format

Text documentation is output.

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

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

Data files

The original data for the documentation can be found in: http://emboss.sourceforge.net/apps/ but please note that this is the documentation for the current development version. The documentation for your release should be nistalled somewhere on your system.

Notes

The documentation for your own release is included as HTML pages in the EMBOSS distribution and may be available at your site. The same documentation is also available however through the program tfm as plain text. The documentation for all current and some past releases is provided by the developers at http://emboss.sourceforge.net/apps/. All EMBOSS programs should be adequately described. If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@emboss.open-bio.org).

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

Paged text output to the screen

tfm is unusual for an EMBOSS program in that it expects to be used interactively and so it displays the documentation text a page at a time, pausing after every page for the user to press the SPACE bar on their keyboard, i.e. it uses the UNIX program more to display the information. This behaviour can be turned off by using the qualifier -nomore.

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

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

References

None.

Warnings

None.

Diagnostic Error Messages

tfm will warn you if you have supplied the name of a program which is not documented yet or which doesn't exist in EMBOSS.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
infoalign Display basic information about a multiple sequence alignment
infobase Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue
infoseq Display basic information about sequences
seealso Finds programs with similar function to a specified program
showdb Displays information on configured databases
textsearch Search the textual description of sequence(s)
whichdb Search all sequence databases for an entry and retrieve it
wossname Finds programs by keywords in their short description

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

Written: 4 Aug 2000.

Target users

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

Comments

None