EMBOSS protocols

EMBOSS specifications

Information


Unique identifier OMICS_21165
Name EMBOSS
Alternative names European Molecular Biology Open Software Suite, EMBOSS explorer, Jemboss, wEMBOSS
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Version 6.6.0
Stability Stable
Maintained Yes

Subtools


  • aaindexextract
  • abiview
  • acdc
  • acdpretty
  • acdtable
  • acdtrace
  • acdvalid
  • aligncopy
  • aligncopypair
  • antigenic
  • assemblyget
  • backtranambig
  • backtranseq
  • banana
  • biosed
  • btwisted
  • cachedas
  • cachedbfetch
  • cacheebeyesearch
  • cacheensembl
  • cai
  • chaos
  • charge
  • checktrans
  • chips
  • cirdna
  • codcmp
  • codcopy
  • coderet
  • compseq
  • cons
  • consambig
  • cpgplot
  • cpgreport
  • cusp
  • cutgextract
  • cutseq
  • dan
  • dbiblast
  • dbifasta
  • dbiflat
  • dbigcg
  • dbtell
  • dbxcompress
  • dbxedam
  • dbxfasta
  • dbxflat
  • dbxgcg
  • dbxobo
  • dbxreport
  • dbxresource
  • dbxstat
  • dbxtax
  • dbxuncompress
  • degapseq
  • density
  • descseq
  • diffseq
  • distmat
  • dotmatcher
  • dotpath
  • dottup
  • dreg
  • drfinddata
  • drfindformat
  • drfindid
  • drfindresource
  • drget
  • drtext
  • edamdef
  • edamhasinput
  • edamhasoutput
  • edamisformat
  • edamisid
  • edamname
  • edialign
  • einverted
  • embossdata
  • embossupdate
  • embossversion
  • emma
  • emowse
  • entret
  • epestfind
  • eprimer3
  • eprimer32
  • equicktandem
  • est2genome
  • etandem
  • extractalign
  • extractfeat
  • extractseq
  • featcopy
  • featmerge
  • featreport
  • feattext
  • findkm
  • freak
  • fuzznuc
  • fuzzpro
  • fuzztran
  • garnier
  • geecee
  • getorf
  • godef
  • goname
  • helixturnhelix
  • hmoment
  • iep
  • infoalign
  • infoassembly
  • infobase
  • inforesidue
  • infoseq
  • Isochore
  • jaspextract
  • jaspscan
  • lindna
  • listor
  • makenucseq
  • makeprotseq
  • marscan
  • maskambignuc
  • maskambigprot
  • maskfeat
  • maskseq
  • matcher
  • megamerger
  • merger
  • msbar
  • mwcontam
  • mwfilter
  • needle
  • needleall
  • newcpgreport
  • newcpgseek
  • newseq
  • nohtml
  • noreturn
  • nospace
  • notab
  • notseq
  • nthseq
  • nthseqset
  • octanol
  • oddcomp
  • ontocount
  • ontocount
  • ontoget
  • ontogetcommon
  • ontogetdown
  • ontogetobsolete
  • ontogetroot
  • ontogetsibs
  • ontogetup
  • ontotext
  • palindrome
  • pasteseq
  • patmatdb
  • patmatmotifs
  • pepcoil
  • pepdigest
  • pepinfo
  • pepnet
  • pepstats
  • pepwheel
  • pepwindow
  • pepwindowall
  • plotcon
  • plotorf
  • polydot
  • preg
  • prettyplot
  • prettyseq
  • primersearch
  • printsextract
  • profit
  • prophecy
  • prophet
  • prosextract
  • pscan
  • psiphi
  • rebaseextract
  • recoder
  • redata
  • refseqget
  • remap
  • restover
  • restrict
  • revseq
  • seealso
  • seqcount
  • seqmatchall
  • seqret
  • seqretsetall
  • seqretsplit
  • seqxref
  • seqxrefget
  • showalign
  • showdb
  • showfeat
  • showorf
  • showpep
  • showseq
  • shuffleseq
  • silent
  • sirna
  • sixpack
  • sizeseq
  • skipseq
  • splitter
  • stretcher
  • stssearch
  • supermatcher
  • syco
  • taxget
  • taxgetdown
  • taxgetrank
  • taxgetspecies
  • taxgetup
  • tcode
  • textsearch
  • tfextract
  • tfscan
  • tranalign
  • transeq
  • trimest
  • trimseq
  • twofeat
  • union
  • vectorstrip
  • water
  • whichdb
  • wobble
  • wordcount
  • wordfinder
  • wordmatch
  • wossdata
  • wossinput
  • wossname
  • wossoperation
  • wossoutput
  • wossparam
  • wosstopic
  • yank

Versioning


Add your version

Documentation


Maintainers


  • person_outline Tim Carver <>
  • person_outline Tim Carver <>

Additional information


http://imed.med.ucm.es/EMBOSS/

Publications for European Molecular Biology Open Software Suite

EMBOSS IN pipelines

 (8)
2017
PMCID: 5225507
PMID: 28073340
DOI: 10.1186/s12864-016-3457-9

[…] file 5: table s4), nucleotide sequences from broad gene annotations of m1.001 published previously [69] were aligned against the c. sublineolum genome using exonerate version 2.2.0 (model est2genome) [133] (additional file 5: table s4). a gene sequence was considered non-unique if there was an alignment with at least 40% of the possible score for a sequence of that length. […]

2017
PMCID: 5487208
PMID: 28653624
DOI: 10.7554/eLife.26875.027

[…] leaving 63 unique sequences for phylogenetic inference. we pairwise aligned each sequence to the a/brisbane/10/2007 (h3n2) coding sequence (genbank accession cy035022) using the program needle from emboss 6.6.0 (rice et al., 2000), which implements a needleman-wunsch alignment. we used raxml 8.2.3 (stamatakis, 2014) to infer a phylogeny from this alignment using a gtrcat codon-substitution […]

2017
PMCID: 5490200
PMID: 28649982
DOI: 10.1038/ncomms15924

[…] fig. 8 for completion. for display on the heat map, one representative sequence of each allele type was chosen. pairwise alignments were performed with the needleman–wunsch algorithm in the emboss package (v. 6.6.0.0) (ref. 59). multiple sequence alignments were performed for each regulatory region (promoter and 5′utr, exons 2–3, and 3′utr) using muscle (v3.8.31) (ref. 56) […]

2016
PMCID: 4726470
PMID: 26808150
DOI: 10.1371/journal.pone.0147849

[…] nr, swiss-prot, gene ontology (go), cluster of orthologous groups of proteins (cog), kyoto encyclopedia of genes and genomes (kegg) databases. the open reading frames (orfs) were predicted by the getorf program., the clean data were mapped to the unigene library using bowtie [27]. then, the read count for each gene was obtained from the mapping results by rsem [28]. fpkm [29] for each unigene […]

2016
PMCID: 4793754
PMID: 26984180
DOI: 10.1186/s12864-015-2350-2

[…] the datasets analyzed in this study are summarized in table 1., next, a bioinformatics pipeline was developed to identify candidate paralogs by linking several complementary algorithms. first, the getorf program [32] was used to identify all possible open reading frames (orfs) for each gm and tc sequence. next, the longorf perl script was used to select the longest orf for each sequence. […]

EMBOSS institution(s)
MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge, UK

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