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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


No version available

Documentation


Maintainers


  • person_outline Richard Durbin
  • person_outline John Chodera
  • person_outline Tim Carver
  • person_outline Alan Bleasby
  • person_outline Ian Longden
  • person_outline Mahmut Uludag
  • person_outline Peter Rice

Additional information


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

Publications for European Molecular Biology Open Software Suite

EMBOSS citations

 (2858)
library_books

Intraperitoneal administration of the anti IL 23 antibody prevents the establishment of intestinal nematodes in mice

2018
Sci Rep
PMCID: 5958071
PMID: 29773890
DOI: 10.1038/s41598-018-26194-x

[…] alysed by quantitative real-time PCR (qPCR). For this, 50 ng of each cDNA were amplified using primer pairs and probes specific for the respective cytokine, which were specifically designed using the eprimer3 software, as described in Table . The primer concentration was optimised and dissociation curves were generated for each pair of primers to verify the amplification of a single PCR product. T […]

call_split

Detection of Anopheles rivulorum like, a member of the Anopheles funestus group, in South Africa

2018
Malar J
PMCID: 5952852
PMID: 29764433
DOI: 10.1186/s12936-018-2353-y
call_split See protocol

[…] version 7.2.5 []. The resulting sequences of the 3 specimens were compared to each other by using the Muscle multiple sequence alignment [] and a consensus sequence was established. Subsequently, the Emboss Needle pairwise sequence alignment tool [] was used to compare the consensus sequence with An. rivulorum-like sequences with the following GenBank accession numbers: KR014818 [], JN994147 [] an […]

library_books

Immunoprofiling of Chlamydia trachomatis using whole proteome microarrays generated by on chip in situ expression

2018
Sci Rep
PMCID: 5951824
PMID: 29760479
DOI: 10.1038/s41598-018-25918-3

[…] range of either 45 °C to 55 °C or 55 °C to 65 °C were selected. If no suitable primer was found, primer sequences starting from positions one or two triplets inside the product were considered. With fuzznuc (EMBOSS, http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html) the final primer pairs were checked for uniqueness of their sequence, and the product length was calculated. To all 5′ […]

library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] ferences in codon preferences between ZIKV lineages, employing a PCA in codon counts, which were calculated with Seqin{R}. Codon usage biases - We calculated the effective number of codons (ENC) with Emboss v6.60 (http://emboss.sourceforge.net/) and the proportion of guanine-cytosine content in the third base of the codons (GC3), using the Seqin{R} program to evaluate the codon usage bias (CUB). T […]

library_books

A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation

2018
Sci Rep
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] mbers, the number of sites that are identical between the OCIAD1 and OCIAD2 human sequences with that of their counterparts in birds, reptiles, amphibians, fish and other mammals were retrieved using EMBOSS Needle (https://www.ebi.ac.uk/Tools/psa/emboss_needle/). The difference between number of identical sites and the length of the protein sequence in the respective species was calculated and sca […]

library_books

An optimal set of features for predicting type IV secretion system effector proteins for a subset of species based on a multi level feature selection approach

2018
PLoS One
PMCID: 5942808
PMID: 29742157
DOI: 10.1371/journal.pone.0197041

[…] phila, appears to have a significant impact on the probability of effector prediction as both features calculated using different methods have been selected in our feature set. For L. pneumophila the pepcoil hitcount (the number of coiled coil domains) and pepcoil length (the total length of coiled coil domains), the averages are 0.64 and 20.1 for effectors, respectively, compared to 0.1 and 3.9 f […]

Citations

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

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