EMBOSS Applications
Application	Description	Documentation
abiview	Display the trace in an ABI sequencer file	abiview
aligncopy	Read and write alignments	aligncopy
aligncopypair	Read and write pairs from alignments	aligncopypair
antigenic	Find antigenic sites in proteins	antigenic
assemblyget	Get assembly of sequence reads	assemblyget
backtranambig	Back-translate a protein sequence to ambiguous nucleotide sequence	backtranambig
backtranseq	Back-translate a protein sequence to a nucleotide sequence	backtranseq
banana	Plot bending and curvature data for B-DNA	banana
biosed	Replace or delete sequence sections	biosed
btwisted	Calculate the twisting in a B-DNA sequence	btwisted
cai	Calculate codon adaptation index	cai
chaos	Draw a chaos game representation plot for a nucleotide sequence	chaos
charge	Draw a protein charge plot	charge
checktrans	Report STOP codons and ORF statistics of a protein	checktrans
chips	Calculate Nc codon usage statistic	chips
cirdna	Draw circular map of DNA constructs	cirdna
codcmp	Codon usage table comparison	codcmp
codcopy	Copy and reformat a codon usage table	codcopy
coderet	Extract CDS, mRNA and translations from feature tables	coderet
compseq	Calculate the composition of unique words in sequences	compseq
cons	Create a consensus sequence from a multiple alignment	cons
consambig	Create an ambiguous consensus sequence from a multiple alignment	consambig
cpgplot	Identify and plot CpG islands in nucleotide sequence(s)	cpgplot
cpgreport	Identify and report CpG-rich regions in nucleotide sequence(s)	cpgreport
cusp	Create a codon usage table from nucleotide sequence(s)	cusp
cutgextract	Extract codon usage tables from CUTG database	cutgextract
cutseq	Remove a section from a sequence	cutseq
dan	Calculate nucleic acid melting temperature	dan
degapseq	Remove non-alphabetic (e.g. gap) characters from sequences	degapseq
density	Draw a nucleic acid density plot	density
descseq	Alter the name or description of a sequence	descseq
diffseq	Compare and report features of two similar sequences	diffseq
distmat	Create a distance matrix from a multiple sequence alignment	distmat
dotmatcher	Draw a threshold dotplot of two sequences	dotmatcher
dotpath	Draw a non-overlapping wordmatch dotplot of two sequences	dotpath
dottup	Display a wordmatch dotplot of two sequences	dottup
dreg	Regular expression search of nucleotide sequence(s)	dreg
drtext	Get data resource entries complete text	drtext
edialign	Local multiple alignment of sequences	edialign
einverted	Find inverted repeats in nucleotide sequences	einverted
embossdata	Find and retrieve EMBOSS data files	embossdata
embossversion	Report the current EMBOSS version number	embossversion
emma	Multiple sequence alignment (ClustalW wrapper)	emma
emowse	Search protein sequences by digest fragment molecular weight	emowse
entret	Retrieve sequence entries from flatfile databases and files	entret
epestfind	Find PEST motifs as potential proteolytic cleavage sites	epestfind
eprimer3	Pick PCR primers and hybridization oligos	eprimer3
eprimer32	Pick PCR primers and hybridization oligos	eprimer32
equicktandem	Find tandem repeats in nucleotide sequences	equicktandem
est2genome	Align EST sequences to genomic DNA sequence	est2genome
etandem	Find tandem repeats in a nucleotide sequence	etandem
extractalign	Extract regions from a sequence alignment	extractalign
extractfeat	Extract features from sequence(s)	extractfeat
extractseq	Extract regions from a sequence	extractseq
featcopy	Read and write a feature table	featcopy
featmerge	Merge two overlapping feature tables	featmerge
featreport	Read and write a feature table	featreport
feattext	Return a feature table original text	feattext
findkm	Calculate and plot enzyme reaction data	findkm
freak	Generate residue/base frequency table or plot	freak
fuzznuc	Search for patterns in nucleotide sequences	fuzznuc
fuzzpro	Search for patterns in protein sequences	fuzzpro
fuzztran	Search for patterns in protein sequences (translated)	fuzztran
garnier	Predict protein secondary structure using GOR method	garnier
geecee	Calculate fractional GC content of nucleic acid sequences	geecee
getorf	Find and extract open reading frames (ORFs)	getorf
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences	helixturnhelix
hmoment	Calculate and plot hydrophobic moment for protein sequence(s)	hmoment
iep	Calculate the isoelectric point of proteins	iep
infoalign	Display basic information about a multiple sequence alignment	infoalign
infoassembly	Display information about assemblies	infoassembly
infobase	Return information on a given nucleotide base	infobase
inforesidue	Return information on a given amino acid residue	inforesidue
infoseq	Display basic information about sequences	infoseq
isochore	Plot isochores in DNA sequences	isochore
jaspscan	Scan DNA sequences for transcription factors	jaspscan
lindna	Draw linear maps of DNA constructs	lindna
listor	Write a list file of the logical OR of two sets of sequences	listor
makenucseq	Create random nucleotide sequences	makenucseq
makeprotseq	Create random protein sequences	makeprotseq
marscan	Find matrix/scaffold recognition (MRS) signatures in DNA sequences	marscan
maskambignuc	Mask all ambiguity characters in nucleotide sequences with N	maskambignuc
maskambigprot	Mask all ambiguity characters in protein sequences with X	maskambigprot
maskfeat	Write a sequence with masked features	maskfeat
maskseq	Write a sequence with masked regions	maskseq
matcher	Waterman-Eggert local alignment of two sequences	matcher
megamerger	Merge two large overlapping DNA sequences	megamerger
merger	Merge two overlapping sequences	merger
msbar	Mutate a sequence	msbar
mwcontam	Find weights common to multiple molecular weights files	mwcontam
mwfilter	Filter noisy data from molecular weights file	mwfilter
needle	Needleman-Wunsch global alignment of two sequences	needle
needleall	Many-to-many pairwise alignments of two sequence sets	needleall
newcpgreport	Identify CpG islands in nucleotide sequence(s)	newcpgreport
newcpgseek	Identify and report CpG-rich regions in nucleotide sequence(s)	newcpgseek
newseq	Create a sequence file from a typed-in sequence	newseq
notseq	Write to file a subset of an input stream of sequences	notseq
nthseq	Write to file a single sequence from an input stream of sequences	nthseq
nthseqset	Read and write (return) one set of sequences from many	nthseqset
octanol	Draw a White-Wimley protein hydropathy plot	octanol
oddcomp	Identify proteins with specified sequence word composition	oddcomp
palindrome	Find inverted repeats in nucleotide sequence(s)	palindrome
pasteseq	Insert one sequence into another	pasteseq
patmatdb	Search protein sequences with a sequence motif	patmatdb
patmatmotifs	Scan a protein sequence with motifs from the PROSITE database	patmatmotifs
pepcoil	Predict coiled coil regions in protein sequences	pepcoil
pepdigest	Report on protein proteolytic enzyme or reagent cleavage sites	pepdigest
pepinfo	Plot amino acid properties of a protein sequence in parallel	pepinfo
pepnet	Draw a helical net for a protein sequence	pepnet
pepstats	Calculate statistics of protein properties	pepstats
pepwheel	Draw a helical wheel diagram for a protein sequence	pepwheel
pepwindow	Draw a hydropathy plot for a protein sequence	pepwindow
pepwindowall	Draw Kyte-Doolittle hydropathy plot for a protein alignment	pepwindowall
plotcon	Plot conservation of a sequence alignment	plotcon
plotorf	Plot potential open reading frames in a nucleotide sequence	plotorf
polydot	Draw dotplots for all-against-all comparison of a sequence set	polydot
preg	Regular expression search of protein sequence(s)	preg
prettyplot	Draw a sequence alignment with pretty formatting	prettyplot
prettyseq	Write a nucleotide sequence and its translation to file	prettyseq
primersearch	Search DNA sequences for matches with primer pairs	primersearch
printsextract	Extract data from PRINTS database for use by pscan	printsextract
profit	Scan one or more sequences with a simple frequency matrix	profit
prophecy	Create frequency matrix or profile from a multiple alignment	prophecy
prophet	Scan one or more sequences with a Gribskov or Henikoff profile	prophet
prosextract	Process the PROSITE motif database for use by patmatmotifs	prosextract
pscan	Scan protein sequence(s) with fingerprints from the PRINTS database	pscan
psiphi	Calculates phi and psi torsion angles from protein coordinates	psiphi
rebaseextract	Process the REBASE database for use by restriction enzyme applications	rebaseextract
recoder	Find restriction sites to remove (mutate) with no translation change	recoder
redata	Retrieve information from REBASE restriction enzyme database	redata
refseqget	Get reference sequence	refseqget
remap	Display restriction enzyme binding sites in a nucleotide sequence	remap
restover	Find restriction enzymes producing a specific overhang	restover
restrict	Report restriction enzyme cleavage sites in a nucleotide sequence	restrict
revseq	Reverse and complement a nucleotide sequence	revseq
seealso	Find programs with similar function to a specified program	seealso
seqcount	Read and count sequences	seqcount
seqmatchall	All-against-all word comparison of a sequence set	seqmatchall
seqret	Read and write (return) sequences	seqret
seqretsetall	Read and write (return) many sets of sequences	seqretsetall
seqretsplit	Read sequences and write them to individual files	seqretsplit
seqxref	Retrieve all database cross-references for a sequence entry	seqxref
seqxrefget	Retrieve all cross-referenced data for a sequence entry	seqxrefget
servertell	Display information about a public server	servertell
showalign	Display a multiple sequence alignment in pretty format	showalign
showdb	Display information on configured databases	showdb
showfeat	Display features of a sequence in pretty format	showfeat
showorf	Display a nucleotide sequence and translation in pretty format	showorf
showpep	Display protein sequences with features in pretty format	showpep
showseq	Display sequences with features in pretty format	showseq
shuffleseq	Shuffle a set of sequences maintaining composition	shuffleseq
sigcleave	Report on signal cleavage sites in a protein sequence	sigcleave
silent	Find restriction sites to insert (mutate) with no translation change	silent
sirna	Find siRNA duplexes in mRNA	sirna
sixpack	Display a DNA sequence with 6-frame translation and ORFs	sixpack
sizeseq	Sort sequences by size	sizeseq
skipredundant	Remove redundant sequences from an input set	skipredundant
skipseq	Read and write (return) sequences, skipping first few	skipseq
splitsource	Split sequence(s) into original source sequences	splitsource
splitter	Split sequence(s) into smaller sequences	splitter
stretcher	Needleman-Wunsch rapid global alignment of two sequences	stretcher
stssearch	Search a DNA database for matches with a set of STS primers	stssearch
supermatcher	Calculate approximate local pair-wise alignments of larger sequences	supermatcher
syco	Draw synonymous codon usage statistic plot for a nucleotide sequence	syco
taxget	Get taxon(s)	taxget
taxgetdown	Get descendants of taxon(s)	taxgetdown
taxgetrank	Get parents of taxon(s)	taxgetrank
taxgetspecies	Get all species under taxon(s)	taxgetspecies
taxgetup	Get parents of taxon(s)	taxgetup
tcode	Identify protein-coding regions using Fickett TESTCODE statistic	tcode
textget	Get text data entries	textget
textsearch	Search the textual description of sequence(s)	textsearch
tfextract	Process TRANSFAC transcription factor database for use by tfscan	tfextract
tfm	Display full documentation for an application	tfm
tfscan	Identify transcription factor binding sites in DNA sequences	tfscan
tmap	Predict and plot transmembrane segments in protein sequences	tmap
tranalign	Generate an alignment of nucleic coding regions from aligned proteins	tranalign
transeq	Translate nucleic acid sequences	transeq
trimest	Remove poly-A tails from nucleotide sequences	trimest
trimseq	Remove unwanted characters from start and end of sequence(s)	trimseq
trimspace	Remove extra whitespace from an ASCII text file	trimspace
twofeat	Find neighbouring pairs of features in sequence(s)	twofeat
union	Concatenate multiple sequences into a single sequence	union
variationget	Get sequence variations	variationget
vectorstrip	Remove vectors from the ends of nucleotide sequence(s)	vectorstrip
water	Smith-Waterman local alignment of sequences	water
whichdb	Search all sequence databases for an entry and retrieve it	whichdb
wobble	Plot third base position variability in a nucleotide sequence	wobble
wordcount	Count and extract unique words in molecular sequence(s)	wordcount
wordfinder	Match large sequences against one or more other sequences	wordfinder
wordmatch	Find regions of identity (exact matches) of two sequences	wordmatch
wossname	Find programs by keywords in their short description	wossname
wossoperation	Find programs by EDAM operation	wossoperation
wossoutput	Find programs by EDAM output data	wossoutput
wossparam	Find programs by EDAM parameter	wossparam
wosstopic	Find programs by EDAM topic	wosstopic
yank	Add a sequence reference (a full USA) to a list file	yank