EMBOSS protocols

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Popular tool citations

chevron_left Gene design Protein-coding gene prediction File filtering File format conversion Genome assembly Known transcript quantification Read simulation Multiple amino acid sequence alignment Pairwise nucleotide sequence alignment Protein-DNA interaction prediction Tandem repeat prediction Dihedral angle prediction EST processing Trace visualization/edition File indexation File editing File comparison Motif discovery Annotation Isoelectric point prediction Secondary structure prediction Adapter trimming In silico analysis Figure creation DaaS Ontology querying Dataset search Microbial taxonomy identification Data warehousing systems CpG island prediction Dot plot generation Domain prediction Gene Ontology annotation Hydropathy plot prediction ORF detection Function prediction Libraries/frameworks Protein inference SLiM prediction Cleavage site prediction Pairwise sequence alignment Feature visualization Sequence alignment visualization pKa prediction Solubility prediction Coiled-coil domain prediction Bioinformatics workflows Hydrophobic region prediction Conventional primer design Variant simulation Circular genome visualization Genome visualization Transcription factor binding site prediction Motif scanning Primer quality Multi-omic data integration Translation Backtranslation Restriction site detection File merging File parsing-extraction File splitting File sorting chevron_right
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Associated diseases

Associated diseases

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


Maintainer


  • person_outline Tim Carver <>

Additional information


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

Publications for European Molecular Biology Open Software Suite

EMBOSS in pipelines

 (377)
2018
PMCID: 5693036
PMID: 29061367
DOI: 10.1016/j.ygcen.2017.10.009

[…] for targeting oligonucleotide primer and probe annealing (). similarity was calculated for each probe against the unintended target mrna reverse-complement by the smith-waterman algorithm using emboss water (, ) and found to be 48.9% for ar_gast_ish1 and 60.9% for ar_gast_ish1. blastn (ncbi) returned no unintended chicken targets for either probe. primers for quantification of lbr, ywhaz […]

2018
PMCID: 5764924
PMID: 29326200
DOI: 10.1128/genomeA.01143-17

[…] by the rapid annotations using subsystems technology (rast) version 2.0 server (). trnas were predicted using trnascan-se version 2.0 (), and the nucleotide homology of pvco-5 was determined using emboss stretcher ()., the genome of pvco-5 comprised double-stranded linear dna of 74,325 bp and a g+c content of 38%. the genome of pvco-5 was approximately 77 to 79% homologous […]

2018
PMCID: 5797582
PMID: 29441050
DOI: 10.3389/fmicb.2018.00063

[…] the respective clusters of orthologous groups (cog) category., first, nucleotide sequences of all annotated pseudogenes of our three strains were extracted, and six-frame translated using transeq (emboss suite 6.6.0.0, http://emboss.open-bio.org/; rice et al., ) to capture potential protein domains present in different reading frames (due to frameshifts). the translated sequences were searched […]

2018
PMCID: 5808241
PMID: 29467727
DOI: 10.3389/fmicb.2018.00082

[…] of protein orthologous/homologs was executed by protein family-associated hidden markov models (hmms) based hmmer3 (http://www.ebi.ac.uk/tools/hmmer/). global alignment of proteins were done using emboss needle (http://www.ebi.ac.uk/tools/psa/emboss_needle/) with gap and extension penalties of 10 and 0.5, respectively, and transmembrane predictions were done using phobius […]

2018
PMCID: 5811046
PMID: 29389943
DOI: 10.1371/journal.pcbi.1005987

[…] ~90% when applying more stringent cutoffs of 3.00 and 5.00 to the assymetry score, respectively ()., frequencies of each single and dimer amino acid in protein sequences were calculated using the compseq program from the emboss package []. for each amino acid dimer, an expected frequency was additionally calculated based on the observed frequencies of single amino acids., multiple alignments […]

EMBOSS in publications

 (2415)
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] of the contigs from yph499 and s799 were sorted and renamed after s288c annotation using blast 2.2.29+. for each chromosome, centromeres with sequences identical to those of s288c were marked using emboss. two haploid genome references were combined for use as the reference genome of the “diploid” cell-fusion strains., snps and indels between the s799 and yph499, yph499, and s288c strains […]

PMCID: 5952852
PMID: 29764433
DOI: 10.1186/s12936-018-2353-y

[…] 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 [] […]

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

[…] 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′-ends […]

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

[…] 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). […]

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

[…] 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 […]

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

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