EMBOSS: The Applications (programs)

The Applications (programs)

Introduction

The programs are listed in alphabetical order, divided into four sections. Look at the individual applications or go to the GROUPS page.

Applications in the current release

If you have any comments about any of the programs, mail the EMBOSS open discussion list emboss@embnet.org.
Bug reports should be sent to the EMBOSS Support Team emboss-bug@embnet.org

Program name Author(s) Description

aaindexextract RFCGR Extract data from AAINDEX

abiview RFCGR Reads ABI file and display the trace

acdc Sanger Tests definition files for any EMBOSS application.

antigenic RFCGR Finds antigenic sites in proteins

backtranseq RFCGR Back translate a protein sequence

banana Sanger Bending and Curvature Plot in B-DNA

biosed RFCGR Replace or delete sequence sections

btwisted RFCGR Calculates the twisting in a B-DNA sequence

cai RFCGR CAI codon usage statistic

chaos Sanger Create a chaos plot for a sequence.

charge RFCGR Protein charge plot

checktrans EBI ORF property statistics

chips RFCGR Codon usage statistics

cirdna Norway Draws circular maps of DNA constructs

codcmp RFCGR Codon usage table comparison

coderet RFCGR Extract CDS, mRNA and translations from feature tables

compseq RFCGR Counts the composition of dimer/trimer/etc words in a sequence

cons RFCGR Creates a consensus from multiple alignments

cpgplot RFCGR Plot CpG rich areas

cpgreport RFCGR Reports CpG rich regions

cusp RFCGR Create a codon usage table

cutgextract HGMP Extract data from CUTG

cutseq RFCGR Removes a specified section from a sequence.

dan RFCGR Plot melting temperatures for DNA.

dbiblast Sanger Database indexing for BLAST 1 and 2 indexed databases

dbifasta RFCGR Index a fasta database

dbiflat Sanger Database indexing for flat file databases

dbigcg Sanger Database indexing for GCG formatted databases

degapseq RFCGR Removes gap characters from sequences

descseq RFCGR Alter the name or description of a sequence.

diffseq RFCGR Find differences between nearly identical sequences

digest RFCGR Protein proteolytic enzyme or reagent cleavage digest

distmat RFCGR Creates a distance matrix from multiple alignments

dotmatcher Sanger Produces a dotplot of two sequences.

dotpath RFCGR Displays a non-overlapping wordmatch dotplot of two sequences

dottup Sanger DNA sequence dot plot

dreg Sanger Regular expression search of a nucleotide sequence

einverted Sanger Finds DNA inverted repeats

embossdata RFCGR Finds or fetches the data files read in by the EMBOSS programs

embossversion RFCGR Writes the current EMBOSS version number

emowse RFCGR Protein identification by mass spectrometry

emma RFCGR Multiple alignment program

entret RFCGR Reads and writes (returns) flatfile entries

epestfind Austria Finds PEST motifs as potential proteolytic cleavage sites

eprimer3 RFCGR Picks PCR primers and hybridization oligos

equicktandem Sanger Finds tandem repeats

est2genome Sanger Align EST and genomic DNA sequences

etandem Sanger Looks for tandem repeats in a nucleotide sequence.

extractfeat RFCGR Extract features from a sequence

extractseq RFCGR Extract regions from a sequence.

findkm RFCGR Calculates Km and Vmax for an enzyme reaction

freak RFCGR Residue/base frequency table or plot

fuzznuc RFCGR Nucleic acid pattern search

fuzzpro RFCGR Protein pattern search

fuzztran RFCGR Protein pattern search after translation

garnier EBI Predicts protein secondary structure

geecee Sanger Calculates the fractional GC content of nucleic acid sequences

getorf RFCGR Finds and extracts open reading frames (ORFs)

helixturnhelix RFCGR Finds nucleic acid binding domains.

hmoment RFCGR Hydrophobic moment calculation

iep RFCGR Calculates the isoelectric point of a protein

infoalign RFCGR Information on a multiple sequence alignment

infoseq RFCGR Displays some simple information about sequences

isochore Sanger Plots isochores in large DNA sequences

jembossctl RFCGR Jemboss Authentication Control

lindna Norway Draws linear maps of DNA constructs

listor RFCGR Writes a list file of the logical OR of two sets of sequences

marscan RFCGR Finds MAR/SAR sites in nucleic sequences

maskfeat RFCGR Mask off features of a sequence

maskseq RFCGR Mask off regions of a sequence.

matcher Sanger Local alignment of two sequences

megamerger RFCGR Merge two large overlapping nucleic acid sequences

merger RFCGR Merge two overlapping sequences

msbar RFCGR Mutate sequence beyond all recognition

mwcontam RFCGR Shows molwts that match across a set of files

mwfilter RFCGR Filter noisy molwts from mass spec output

needle RFCGR Needleman-Wunsch global alignment.

newcpgreport EBI Report CpG rich areas

newcpgseek EBI Reports CpG rich regions

newseq RFCGR Type in a short new sequence.

noreturn RFCGR Removes carriage return from ASCII files

notseq RFCGR Excludes a set of sequences and writes out the remaining ones

nthseq RFCGR Writes one sequence from a multiple set of sequences

octanol Sanger Displays protein hydropathy

oddcomp Norway Finds protein sequence regions with a biased composition.

palindrome RFCGR Looks for inverted repeats in a nucleotide sequence.

pasteseq RFCGR Insert one sequence into another.

patmatdb RFCGR Matching a Prosite motif against a Protein Sequence Database.

patmatmotifs RFCGR Compares a protein sequence to the PROSITE motif database.

pepcoil RFCGR Predicts coiled coil regions

pepinfo RFCGR Plots simple amino acid properties in parallel

pepnet RFCGR Protein helical net plot

pepstats RFCGR Protein statistics

pepwheel RFCGR Shows protein sequences as helices

pepwindow Sanger Displays protein hydropathy

pepwindowall Sanger Displays protein hydropathy of a set of sequences

plotcon RFCGR Plots the quality of conservation of a sequence alignment

plotorf RFCGR Plot potential open reading frames

polydot Sanger Multiple dotplot

preg Sanger Regular expression search of a protein sequence

prettyplot Sanger Displays aligned sequences, with colouring and boxing.

prettyseq RFCGR Output sequence with translated ranges

primersearch RFCGR Searches DNA sequences for matches with primer pairs

printsextract RFCGR Preprocesses the PRINTS database for use with the program PSCAN

profit RFCGR Scan a sequence or database with a matrix or profile

prophecy RFCGR Creates matrices/profiles from multiple alignments

prophet RFCGR Gapped alignment for profiles

prosextract RFCGR Extracts ID, AC, and PA lines from the PROSITE motif database.

pscan RFCGR Locates fingerprints (multiple motif features) in a protein sequence.

rebaseextract RFCGR Extract data from REBASE

recoder RFCGR Find and remove restriction sites but maintain the same translation

redata RFCGR Isoschizomers, references and Suppliers for Restriction Enzymes

remap RFCGR Display a sequence with restriction cut sites, translation etc..

restover Sloan-Kettering Cancer Center Finds restriction enzymes that produce a specific overhang

restrict RFCGR Finds Restriction Enzyme Cleavage Sites

revseq RFCGR Reverse and complement a sequence.

seealso RFCGR Finds programs sharing group names

seqmatchall Sanger Does an all-against-all comparison of a set of sequences

seqret Sanger Reads and writes (returns) a sequence.

seqretsplit RFCGR Reads and writes (returns) sequences in individual files

showdb RFCGR Displays information on the currently available databases

showalign RFCGR Display a multiple sequence alignment

showfeat RFCGR Show features of a sequence.

showorf RFCGR Pretty output of DNA translations

showseq RFCGR Display a sequence with features, translation etc

shuffleseq RFCGR Shuffles a set of sequences maintaining composition

sigcleave RFCGR Predicts signal peptide cleavage sites

silent RFCGR Silent mutation restriction enzyme scan

sirna RFCGR Finds siRNA duplexes in mRNA

sixpack LION Display a DNA sequence with 6-frame translation and ORFs

skipseq RFCGR Reads and writes (returns) sequences, skipping the first few

splitter RFCGR Split a sequence into (overlapping) smaller sequences.

stretcher Sanger Global alignment of two sequences.

stssearch Sanger Searches a DNA database for matches with a set of STS primers

supermatcher Sanger Finds a match of a large sequence against one or more sequences

syco RFCGR Synonymous codon usage Gribskov statistic plot

tcode RFCGR Fickett TESTCODE statistic to identify protein-coding DNA

textsearch RFCGR Search sequence documentation text. SRS and Entrez are faster!

tfextract RFCGR Extract data from TRANSFAC

tfm RFCGR Displays a program's help documentation manual

tfscan RFCGR Scans DNA sequences for transcription factors.

tmap Sanger Predict transmembrane proteins

tranalign RFCGR Align nucleic coding regions given the aligned proteins

transeq RFCGR Translates nucleic acid sequences.

trimest RFCGR Trim poly-A tails off EST sequences

trimseq RFCGR Trim ambiguous bits off the ends of sequences

twofeat RFCGR Finds neighbouring pairs of features in sequences

union LION Reads sequence fragments and builds one sequence

vectorstrip RFCGR Strips out DNA between a pair of vector sequences

water RFCGR Smith-Waterman local alignment.

whichdb RFCGR Search all databases for an entry

wobble RFCGR Wobble base plot

wordcount Sanger Counts words of a specified size in a DNA sequence.

wordmatch Sanger Finds all exact matches of a given size between 2 sequences

wossname RFCGR Finds programs by keywords in their one-line documentation.

yank LION Reads a range from a sequence, appends the full USA to a list file

Program name	Author(s)	Description
aaindexextract	RFCGR	Extract data from AAINDEX
abiview	RFCGR	Reads ABI file and display the trace
acdc	Sanger	Tests definition files for any EMBOSS application.
antigenic	RFCGR	Finds antigenic sites in proteins
backtranseq	RFCGR	Back translate a protein sequence
banana	Sanger	Bending and Curvature Plot in B-DNA
biosed	RFCGR	Replace or delete sequence sections
btwisted	RFCGR	Calculates the twisting in a B-DNA sequence
cai	RFCGR	CAI codon usage statistic
chaos	Sanger	Create a chaos plot for a sequence.
charge	RFCGR	Protein charge plot
checktrans	EBI	ORF property statistics
chips	RFCGR	Codon usage statistics
cirdna	Norway	Draws circular maps of DNA constructs
codcmp	RFCGR	Codon usage table comparison
coderet	RFCGR	Extract CDS, mRNA and translations from feature tables
compseq	RFCGR	Counts the composition of dimer/trimer/etc words in a sequence
cons	RFCGR	Creates a consensus from multiple alignments
cpgplot	RFCGR	Plot CpG rich areas
cpgreport	RFCGR	Reports CpG rich regions
cusp	RFCGR	Create a codon usage table
cutgextract	HGMP	Extract data from CUTG
cutseq	RFCGR	Removes a specified section from a sequence.
dan	RFCGR	Plot melting temperatures for DNA.
dbiblast	Sanger	Database indexing for BLAST 1 and 2 indexed databases
dbifasta	RFCGR	Index a fasta database
dbiflat	Sanger	Database indexing for flat file databases
dbigcg	Sanger	Database indexing for GCG formatted databases
degapseq	RFCGR	Removes gap characters from sequences
descseq	RFCGR	Alter the name or description of a sequence.
diffseq	RFCGR	Find differences between nearly identical sequences
digest	RFCGR	Protein proteolytic enzyme or reagent cleavage digest
distmat	RFCGR	Creates a distance matrix from multiple alignments
dotmatcher	Sanger	Produces a dotplot of two sequences.
dotpath	RFCGR	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Sanger	DNA sequence dot plot
dreg	Sanger	Regular expression search of a nucleotide sequence
einverted	Sanger	Finds DNA inverted repeats
embossdata	RFCGR	Finds or fetches the data files read in by the EMBOSS programs
embossversion	RFCGR	Writes the current EMBOSS version number
emowse	RFCGR	Protein identification by mass spectrometry
emma	RFCGR	Multiple alignment program
entret	RFCGR	Reads and writes (returns) flatfile entries
epestfind	Austria	Finds PEST motifs as potential proteolytic cleavage sites
eprimer3	RFCGR	Picks PCR primers and hybridization oligos
equicktandem	Sanger	Finds tandem repeats
est2genome	Sanger	Align EST and genomic DNA sequences
etandem	Sanger	Looks for tandem repeats in a nucleotide sequence.
extractfeat	RFCGR	Extract features from a sequence
extractseq	RFCGR	Extract regions from a sequence.
findkm	RFCGR	Calculates Km and Vmax for an enzyme reaction
freak	RFCGR	Residue/base frequency table or plot
fuzznuc	RFCGR	Nucleic acid pattern search
fuzzpro	RFCGR	Protein pattern search
fuzztran	RFCGR	Protein pattern search after translation
garnier	EBI	Predicts protein secondary structure
geecee	Sanger	Calculates the fractional GC content of nucleic acid sequences
getorf	RFCGR	Finds and extracts open reading frames (ORFs)
helixturnhelix	RFCGR	Finds nucleic acid binding domains.
hmoment	RFCGR	Hydrophobic moment calculation
iep	RFCGR	Calculates the isoelectric point of a protein
infoalign	RFCGR	Information on a multiple sequence alignment
infoseq	RFCGR	Displays some simple information about sequences
isochore	Sanger	Plots isochores in large DNA sequences
jembossctl	RFCGR	Jemboss Authentication Control
lindna	Norway	Draws linear maps of DNA constructs
listor	RFCGR	Writes a list file of the logical OR of two sets of sequences
marscan	RFCGR	Finds MAR/SAR sites in nucleic sequences
maskfeat	RFCGR	Mask off features of a sequence
maskseq	RFCGR	Mask off regions of a sequence.
matcher	Sanger	Local alignment of two sequences
megamerger	RFCGR	Merge two large overlapping nucleic acid sequences
merger	RFCGR	Merge two overlapping sequences
msbar	RFCGR	Mutate sequence beyond all recognition
mwcontam	RFCGR	Shows molwts that match across a set of files
mwfilter	RFCGR	Filter noisy molwts from mass spec output
needle	RFCGR	Needleman-Wunsch global alignment.
newcpgreport	EBI	Report CpG rich areas
newcpgseek	EBI	Reports CpG rich regions
newseq	RFCGR	Type in a short new sequence.
noreturn	RFCGR	Removes carriage return from ASCII files
notseq	RFCGR	Excludes a set of sequences and writes out the remaining ones
nthseq	RFCGR	Writes one sequence from a multiple set of sequences
octanol	Sanger	Displays protein hydropathy
oddcomp	Norway	Finds protein sequence regions with a biased composition.
palindrome	RFCGR	Looks for inverted repeats in a nucleotide sequence.
pasteseq	RFCGR	Insert one sequence into another.
patmatdb	RFCGR	Matching a Prosite motif against a Protein Sequence Database.
patmatmotifs	RFCGR	Compares a protein sequence to the PROSITE motif database.
pepcoil	RFCGR	Predicts coiled coil regions
pepinfo	RFCGR	Plots simple amino acid properties in parallel
pepnet	RFCGR	Protein helical net plot
pepstats	RFCGR	Protein statistics
pepwheel	RFCGR	Shows protein sequences as helices
pepwindow	Sanger	Displays protein hydropathy
pepwindowall	Sanger	Displays protein hydropathy of a set of sequences
plotcon	RFCGR	Plots the quality of conservation of a sequence alignment
plotorf	RFCGR	Plot potential open reading frames
polydot	Sanger	Multiple dotplot
preg	Sanger	Regular expression search of a protein sequence
prettyplot	Sanger	Displays aligned sequences, with colouring and boxing.
prettyseq	RFCGR	Output sequence with translated ranges
primersearch	RFCGR	Searches DNA sequences for matches with primer pairs
printsextract	RFCGR	Preprocesses the PRINTS database for use with the program PSCAN
profit	RFCGR	Scan a sequence or database with a matrix or profile
prophecy	RFCGR	Creates matrices/profiles from multiple alignments
prophet	RFCGR	Gapped alignment for profiles
prosextract	RFCGR	Extracts ID, AC, and PA lines from the PROSITE motif database.
pscan	RFCGR	Locates fingerprints (multiple motif features) in a protein sequence.
rebaseextract	RFCGR	Extract data from REBASE
recoder	RFCGR	Find and remove restriction sites but maintain the same translation
redata	RFCGR	Isoschizomers, references and Suppliers for Restriction Enzymes
remap	RFCGR	Display a sequence with restriction cut sites, translation etc..
restover	Sloan-Kettering Cancer Center	Finds restriction enzymes that produce a specific overhang
restrict	RFCGR	Finds Restriction Enzyme Cleavage Sites
revseq	RFCGR	Reverse and complement a sequence.
seealso	RFCGR	Finds programs sharing group names
seqmatchall	Sanger	Does an all-against-all comparison of a set of sequences
seqret	Sanger	Reads and writes (returns) a sequence.
seqretsplit	RFCGR	Reads and writes (returns) sequences in individual files
showdb	RFCGR	Displays information on the currently available databases
showalign	RFCGR	Display a multiple sequence alignment
showfeat	RFCGR	Show features of a sequence.
showorf	RFCGR	Pretty output of DNA translations
showseq	RFCGR	Display a sequence with features, translation etc
shuffleseq	RFCGR	Shuffles a set of sequences maintaining composition
sigcleave	RFCGR	Predicts signal peptide cleavage sites
silent	RFCGR	Silent mutation restriction enzyme scan
sirna	RFCGR	Finds siRNA duplexes in mRNA
sixpack	LION	Display a DNA sequence with 6-frame translation and ORFs
skipseq	RFCGR	Reads and writes (returns) sequences, skipping the first few
splitter	RFCGR	Split a sequence into (overlapping) smaller sequences.
stretcher	Sanger	Global alignment of two sequences.
stssearch	Sanger	Searches a DNA database for matches with a set of STS primers
supermatcher	Sanger	Finds a match of a large sequence against one or more sequences
syco	RFCGR	Synonymous codon usage Gribskov statistic plot
tcode	RFCGR	Fickett TESTCODE statistic to identify protein-coding DNA
textsearch	RFCGR	Search sequence documentation text. SRS and Entrez are faster!
tfextract	RFCGR	Extract data from TRANSFAC
tfm	RFCGR	Displays a program's help documentation manual
tfscan	RFCGR	Scans DNA sequences for transcription factors.
tmap	Sanger	Predict transmembrane proteins
tranalign	RFCGR	Align nucleic coding regions given the aligned proteins
transeq	RFCGR	Translates nucleic acid sequences.
trimest	RFCGR	Trim poly-A tails off EST sequences
trimseq	RFCGR	Trim ambiguous bits off the ends of sequences
twofeat	RFCGR	Finds neighbouring pairs of features in sequences
union	LION	Reads sequence fragments and builds one sequence
vectorstrip	RFCGR	Strips out DNA between a pair of vector sequences
water	RFCGR	Smith-Waterman local alignment.
whichdb	RFCGR	Search all databases for an entry
wobble	RFCGR	Wobble base plot
wordcount	Sanger	Counts words of a specified size in a DNA sequence.
wordmatch	Sanger	Finds all exact matches of a given size between 2 sequences
wossname	RFCGR	Finds programs by keywords in their one-line documentation.
yank	LION	Reads a range from a sequence, appends the full USA to a list file

EMBASSY

EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL).
Programs which have been included from third parties who have their own licencing terms are kept apart under the EMBASSY grouping.

This allows the EMBOSS libraries to link to other software, and only requires that software to have an LGPL-compatible licence. Phylip, for example, fits this model.

But, to the user they do look exactly like EMBOSS aplications.

EMBASSY - PHYLIP

Program name	Author(s)	Description
eclique	Sanger	Conversion of PHYLIP's clique
econsense	Sanger	Conversion of PHYLIP's consense
econtml	Sanger	Conversion of PHYLIP's contml
econtrast	Sanger	Conversion of PHYLIP's contrast
ednacomp	Sanger	Conversion of PHYLIP's dnacomp
ednadist	Sanger	Conversion of PHYLIP's dnadist
ednainvar	Sanger	Conversion of PHYLIP's dnainvar
ednaml	Sanger	Conversion of PHYLIP's dnaml
ednamlk	Sanger	Conversion of PHYLIP's dnamlk
ednapars	Sanger	Conversion of PHYLIP's dnapars
ednapenny	Sanger	Conversion of PHYLIP's dnapenny
edollop	Sanger	Conversion of PHYLIP's dollop
edolpenny	Sanger	Conversion of PHYLIP's dolpenny
efactor	Sanger	Conversion of PHYLIP's factor
efitch	Sanger	Conversion of PHYLIP's fitch
egendist	Sanger	Conversion of PHYLIP's gendist
ekitsch	Sanger	Conversion of PHYLIP's kitsch
emix	Sanger	Conversion of PHYLIP's mix
eneighbor	Sanger	Conversion of PHYLIP's neighbor
epenny	Sanger	Conversion of PHYLIP's penny
eprotdist	Sanger	Conversion of PHYLIP's protdist
eprotpars	Sanger	Conversion of PHYLIP's protpars
erestml	Sanger	Conversion of PHYLIP's restml
eseqboot	Sanger	Conversion of PHYLIP's seqboot

EMBASSY - DOMAINATRIX

Program name	Author(s)	Description
pdbparse	RFCGR	Parses PDB files and writes CCF files (clean coordinate files) for proteins.
pdbplus	RFCGR	Add records for residue solvent accessibility and secondary structure to a clean coordinate file.
domainer	RFCGR	Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file).
scopparse	RFCGR	Reads raw SCOP classification files and writes a DCF file (domain classification file).
domainreso	RFCGR	Removes low resolution domains from a DCF file (domain classification file).
domainseqs	RFCGR	Adds sequence records to a DCF file (domain classification file).
domainnr	RFCGR	Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS.
domainrep	RFCGR	Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first.
domainalign	RFCGR	Generates structure-based sequence alignments for nodes in a DCF file (domain classification file).
seqsearch	RFCGR	Generate database hits (sequences) from a DAF file (domain alignment file) or other sequences by using PSI-BLAST.
seqfraggle	RFCGR	Removes fragments from DHF files (domain hits files) or other files of sequences.
seqsort	RFCGR	Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification.
seqnr	RFCGR	Removes redundancy from DHF files (domain hits files) or other files of sequences.
seqalign	RFCGR	Reads a DAF file (domain alignment file) and a DHF (domain hits file) and writes a DAF file extended with the hits.
siggen	RFCGR	Generates a sparse protein signature from an alignment and residue contact data.
libgen	RFCGR	Generates various type of discriminator for each alignment in a directory.
libscan	RFCGR	Generates hits (sequences in a domain hits file) from searches of various types of discriminator (HMMs, profiles etc) against a sequence database. Or generates hits from screening sequences against a library of such discriminators.
rocon	RFCGR	Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a "hits file" for the hits, which are classified and rank-ordered on the basis of score.
rocplot	RFCGR	A generic and flexible tool for interpretation and graphical display of the performance of predictive methods using receiver Operator Characteristic (ROC) analysis.
contacts	RFCGR	Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data.
interface	RFCGR	Reads protein CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data.
sites	RFCGR	Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file).
hetparse	RFCGR	Converts raw dictionary of heterogen groups to a file in EMBL-like format.
pdbtosp	RFCGR	Convert raw swissprot:PDB equivalence file to EMBL-like format.
cathparse	RFCGR	Reads raw CATH classification files and writes DCF file (domain classification file).

EMBASSY - OTHERS