EMBOSS Applications
abiviewDisplay the trace in an ABI sequencer fileabiview
aligncopyRead and write alignmentsaligncopy
aligncopypairRead and write pairs from alignmentsaligncopypair
antigenicFind antigenic sites in proteinsantigenic
assemblygetGet assembly of sequence readsassemblyget
backtranambigBack-translate a protein sequence to ambiguous nucleotide sequencebacktranambig
backtranseqBack-translate a protein sequence to a nucleotide sequencebacktranseq
bananaPlot bending and curvature data for B-DNAbanana
biosedReplace or delete sequence sectionsbiosed
btwistedCalculate the twisting in a B-DNA sequencebtwisted
caiCalculate codon adaptation indexcai
chaosDraw a chaos game representation plot for a nucleotide sequencechaos
chargeDraw a protein charge plotcharge
checktransReport STOP codons and ORF statistics of a proteinchecktrans
chipsCalculate Nc codon usage statisticchips
cirdnaDraw circular map of DNA constructscirdna
codcmpCodon usage table comparisoncodcmp
codcopyCopy and reformat a codon usage tablecodcopy
coderetExtract CDS, mRNA and translations from feature tablescoderet
compseqCalculate the composition of unique words in sequencescompseq
consCreate a consensus sequence from a multiple alignmentcons
consambigCreate an ambiguous consensus sequence from a multiple alignmentconsambig
cpgplotIdentify and plot CpG islands in nucleotide sequence(s)cpgplot
cpgreportIdentify and report CpG-rich regions in nucleotide sequence(s)cpgreport
cuspCreate a codon usage table from nucleotide sequence(s)cusp
cutgextractExtract codon usage tables from CUTG databasecutgextract
cutseqRemove a section from a sequencecutseq
danCalculate nucleic acid melting temperaturedan
degapseqRemove non-alphabetic (e.g. gap) characters from sequencesdegapseq
densityDraw a nucleic acid density plotdensity
descseqAlter the name or description of a sequencedescseq
diffseqCompare and report features of two similar sequencesdiffseq
distmatCreate a distance matrix from a multiple sequence alignmentdistmat
dotmatcherDraw a threshold dotplot of two sequencesdotmatcher
dotpathDraw a non-overlapping wordmatch dotplot of two sequencesdotpath
dottupDisplay a wordmatch dotplot of two sequencesdottup
dregRegular expression search of nucleotide sequence(s)dreg
drtextGet data resource entries complete textdrtext
edialignLocal multiple alignment of sequencesedialign
einvertedFind inverted repeats in nucleotide sequenceseinverted
embossdataFind and retrieve EMBOSS data filesembossdata
embossversionReport the current EMBOSS version numberembossversion
emmaMultiple sequence alignment (ClustalW wrapper)emma
emowseSearch protein sequences by digest fragment molecular weightemowse
entretRetrieve sequence entries from flatfile databases and filesentret
epestfindFind PEST motifs as potential proteolytic cleavage sitesepestfind
eprimer3Pick PCR primers and hybridization oligoseprimer3
eprimer32Pick PCR primers and hybridization oligoseprimer32
equicktandemFind tandem repeats in nucleotide sequencesequicktandem
est2genomeAlign EST sequences to genomic DNA sequenceest2genome
etandemFind tandem repeats in a nucleotide sequenceetandem
extractalignExtract regions from a sequence alignmentextractalign
extractfeatExtract features from sequence(s)extractfeat
extractseqExtract regions from a sequenceextractseq
featcopyRead and write a feature tablefeatcopy
featmergeMerge two overlapping feature tablesfeatmerge
featreportRead and write a feature tablefeatreport
feattextReturn a feature table original textfeattext
findkmCalculate and plot enzyme reaction datafindkm
freakGenerate residue/base frequency table or plotfreak
fuzznucSearch for patterns in nucleotide sequencesfuzznuc
fuzzproSearch for patterns in protein sequencesfuzzpro
fuzztranSearch for patterns in protein sequences (translated)fuzztran
garnierPredict protein secondary structure using GOR methodgarnier
geeceeCalculate fractional GC content of nucleic acid sequencesgeecee
getorfFind and extract open reading frames (ORFs)getorf
helixturnhelixIdentify nucleic acid-binding motifs in protein sequenceshelixturnhelix
hmomentCalculate and plot hydrophobic moment for protein sequence(s)hmoment
iepCalculate the isoelectric point of proteinsiep
infoalignDisplay basic information about a multiple sequence alignmentinfoalign
infoassemblyDisplay information about assembliesinfoassembly
infobaseReturn information on a given nucleotide baseinfobase
inforesidueReturn information on a given amino acid residueinforesidue
infoseqDisplay basic information about sequencesinfoseq
isochorePlot isochores in DNA sequencesisochore
jaspscanScan DNA sequences for transcription factorsjaspscan
lindnaDraw linear maps of DNA constructslindna
listorWrite a list file of the logical OR of two sets of sequenceslistor
makenucseqCreate random nucleotide sequencesmakenucseq
makeprotseqCreate random protein sequencesmakeprotseq
marscanFind matrix/scaffold recognition (MRS) signatures in DNA sequencesmarscan
maskambignucMask all ambiguity characters in nucleotide sequences with Nmaskambignuc
maskambigprotMask all ambiguity characters in protein sequences with Xmaskambigprot
maskfeatWrite a sequence with masked featuresmaskfeat
maskseqWrite a sequence with masked regionsmaskseq
matcherWaterman-Eggert local alignment of two sequencesmatcher
megamergerMerge two large overlapping DNA sequencesmegamerger
mergerMerge two overlapping sequencesmerger
msbarMutate a sequencemsbar
mwcontamFind weights common to multiple molecular weights filesmwcontam
mwfilterFilter noisy data from molecular weights filemwfilter
needleNeedleman-Wunsch global alignment of two sequencesneedle
needleallMany-to-many pairwise alignments of two sequence setsneedleall
newcpgreportIdentify CpG islands in nucleotide sequence(s)newcpgreport
newcpgseekIdentify and report CpG-rich regions in nucleotide sequence(s)newcpgseek
newseqCreate a sequence file from a typed-in sequencenewseq
notseqWrite to file a subset of an input stream of sequencesnotseq
nthseqWrite to file a single sequence from an input stream of sequencesnthseq
nthseqsetRead and write (return) one set of sequences from manynthseqset
octanolDraw a White-Wimley protein hydropathy plotoctanol
oddcompIdentify proteins with specified sequence word compositionoddcomp
palindromeFind inverted repeats in nucleotide sequence(s)palindrome
pasteseqInsert one sequence into anotherpasteseq
patmatdbSearch protein sequences with a sequence motifpatmatdb
patmatmotifsScan a protein sequence with motifs from the PROSITE databasepatmatmotifs
pepcoilPredict coiled coil regions in protein sequencespepcoil
pepdigestReport on protein proteolytic enzyme or reagent cleavage sitespepdigest
pepinfoPlot amino acid properties of a protein sequence in parallelpepinfo
pepnetDraw a helical net for a protein sequencepepnet
pepstatsCalculate statistics of protein propertiespepstats
pepwheelDraw a helical wheel diagram for a protein sequencepepwheel
pepwindowDraw a hydropathy plot for a protein sequencepepwindow
pepwindowallDraw Kyte-Doolittle hydropathy plot for a protein alignmentpepwindowall
plotconPlot conservation of a sequence alignmentplotcon
plotorfPlot potential open reading frames in a nucleotide sequenceplotorf
polydotDraw dotplots for all-against-all comparison of a sequence setpolydot
pregRegular expression search of protein sequence(s)preg
prettyplotDraw a sequence alignment with pretty formattingprettyplot
prettyseqWrite a nucleotide sequence and its translation to fileprettyseq
primersearchSearch DNA sequences for matches with primer pairsprimersearch
printsextractExtract data from PRINTS database for use by pscanprintsextract
profitScan one or more sequences with a simple frequency matrixprofit
prophecyCreate frequency matrix or profile from a multiple alignmentprophecy
prophetScan one or more sequences with a Gribskov or Henikoff profileprophet
prosextractProcess the PROSITE motif database for use by patmatmotifsprosextract
pscanScan protein sequence(s) with fingerprints from the PRINTS databasepscan
psiphiCalculates phi and psi torsion angles from protein coordinatespsiphi
rebaseextractProcess the REBASE database for use by restriction enzyme applicationsrebaseextract
recoderFind restriction sites to remove (mutate) with no translation changerecoder
redataRetrieve information from REBASE restriction enzyme databaseredata
refseqgetGet reference sequencerefseqget
remapDisplay restriction enzyme binding sites in a nucleotide sequenceremap
restoverFind restriction enzymes producing a specific overhangrestover
restrictReport restriction enzyme cleavage sites in a nucleotide sequencerestrict
revseqReverse and complement a nucleotide sequencerevseq
seealsoFind programs with similar function to a specified programseealso
seqcountRead and count sequencesseqcount
seqmatchallAll-against-all word comparison of a sequence setseqmatchall
seqretRead and write (return) sequencesseqret
seqretsetallRead and write (return) many sets of sequencesseqretsetall
seqretsplitRead sequences and write them to individual filesseqretsplit
seqxrefRetrieve all database cross-references for a sequence entryseqxref
seqxrefgetRetrieve all cross-referenced data for a sequence entryseqxrefget
servertellDisplay information about a public serverservertell
showalignDisplay a multiple sequence alignment in pretty formatshowalign
showdbDisplay information on configured databasesshowdb
showfeatDisplay features of a sequence in pretty formatshowfeat
showorfDisplay a nucleotide sequence and translation in pretty formatshoworf
showpepDisplay protein sequences with features in pretty formatshowpep
showseqDisplay sequences with features in pretty formatshowseq
shuffleseqShuffle a set of sequences maintaining compositionshuffleseq
sigcleaveReport on signal cleavage sites in a protein sequencesigcleave
silentFind restriction sites to insert (mutate) with no translation changesilent
sirnaFind siRNA duplexes in mRNAsirna
sixpackDisplay a DNA sequence with 6-frame translation and ORFssixpack
sizeseqSort sequences by sizesizeseq
skipredundantRemove redundant sequences from an input setskipredundant
skipseqRead and write (return) sequences, skipping first fewskipseq
splitsourceSplit sequence(s) into original source sequencessplitsource
splitterSplit sequence(s) into smaller sequencessplitter
stretcherNeedleman-Wunsch rapid global alignment of two sequencesstretcher
stssearchSearch a DNA database for matches with a set of STS primersstssearch
supermatcherCalculate approximate local pair-wise alignments of larger sequencessupermatcher
sycoDraw synonymous codon usage statistic plot for a nucleotide sequencesyco
taxgetGet taxon(s)taxget
taxgetdownGet descendants of taxon(s)taxgetdown
taxgetrankGet parents of taxon(s)taxgetrank
taxgetspeciesGet all species under taxon(s)taxgetspecies
taxgetupGet parents of taxon(s)taxgetup
tcodeIdentify protein-coding regions using Fickett TESTCODE statistictcode
textgetGet text data entriestextget
textsearchSearch the textual description of sequence(s)textsearch
tfextractProcess TRANSFAC transcription factor database for use by tfscantfextract
tfmDisplay full documentation for an applicationtfm
tfscanIdentify transcription factor binding sites in DNA sequencestfscan
tmapPredict and plot transmembrane segments in protein sequencestmap
tranalignGenerate an alignment of nucleic coding regions from aligned proteinstranalign
transeqTranslate nucleic acid sequencestranseq
trimestRemove poly-A tails from nucleotide sequencestrimest
trimseqRemove unwanted characters from start and end of sequence(s)trimseq
trimspaceRemove extra whitespace from an ASCII text filetrimspace
twofeatFind neighbouring pairs of features in sequence(s)twofeat
unionConcatenate multiple sequences into a single sequenceunion
variationgetGet sequence variationsvariationget
vectorstripRemove vectors from the ends of nucleotide sequence(s)vectorstrip
waterSmith-Waterman local alignment of sequenceswater
whichdbSearch all sequence databases for an entry and retrieve itwhichdb
wobblePlot third base position variability in a nucleotide sequencewobble
wordcountCount and extract unique words in molecular sequence(s)wordcount
wordfinderMatch large sequences against one or more other sequenceswordfinder
wordmatchFind regions of identity (exact matches) of two sequenceswordmatch
wossnameFind programs by keywords in their short descriptionwossname
wossoperationFind programs by EDAM operationwossoperation
wossoutputFind programs by EDAM output datawossoutput
wossparamFind programs by EDAM parameterwossparam
wosstopicFind programs by EDAM topicwosstopic
yankAdd a sequence reference (a full USA) to a list fileyank