EMBOSS pipeline

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


  • prophet
  • 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
  • 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
  • needle
  • pepdigest
  • pepinfo
  • pepnet
  • pepstats
  • pepwheel
  • pepwindow
  • pepwindowall
  • plotcon
  • plotorf
  • polydot
  • preg
  • prettyplot
  • prettyseq
  • primersearch
  • printsextract
  • profit
  • prophecy
  • prosextract
  • pscan
  • 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

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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 citations

 (11)
2017
PMCID: 5634895

[…] the evolution and diversity of 10.1601/nm.3093 strains [14]. phylogrouping was performed in silico using the quadruplex method described by clermont et al. [14] and the primersearch program from the emboss open software suite [15]. 10.1601/nm.3093 bg1 belongs to the phylogroup b1, which is commonly distributed among both bovine commensal and human pathogenic 10.1601/nm.3093 strains [16, 17]., […]

2015
PMCID: 4626756

[…] was retained, and the examined hosts were further restricted to only duck species, to make a sequence set with a size manageable for phylogenetic modeling., sequences from each host were aligned by emboss needle (rice et al. 2000), and maximum-likelihood trees were built by raxml (stamatakis 2006). using these trees and the program path-o-gen (http://tree.bio.ed.ac.uk/software/pathogen/, last […]

2015
PMCID: 4424575

[…] from the opposite end of the molecules. thus, two 41-nt reads were generated for each cdna fragment revealing the sequence information starting from both ends of the original mrna template., emboss needle [43] was used to perform and visualize the global sequence alignment between exfelv and enfelv. the tool was used with the default parameters, version 6.6.0., mapping was done using […]

2012
PMCID: 3521398

[…] image includes a set of pre-installed tools that can be directly accessed upon the creation of the cluster. in the current version of elastichpc, there are about 200 tools, coming from biolinux, emboss [23], samtools [24], fastx [25], ncbi blast toolkit [26-28], and other individual sequence and rna analysis programs. these tools come from the bibiserv and nubios bioinformatics servers. […]

2012
PMCID: 3511272

[…] cds from predicted lgt gene as well as for the rest of protein-coding genes. we generated codon usage tables for lgt genes and for the rest of protein-coding genes using the cusp program from the emboss package. we then used the codcmp program from emboss to compare codon usage in lgt genes and in the rest of protein-coding genes., the 609 non-redundant protein sequences corresponding […]

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

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