WU-BLAST protocols

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WU-BLAST specifications

Information


Unique identifier OMICS_01001
Name WU-BLAST
Alternative names wuBLAST, WU-BLAST2, European Bioinformatics Institute’s WU-Blast2, EBI WU-BLAST2
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Subtool


  • WU-BLASTP

Maintainer


This tool is not available anymore.

Publications for WU-BLAST

WU-BLAST in pipelines

 (32)
2018
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] snp, transposons, genes, gene families, gene annotations, gene names, proteins, and mutant orderings. multiple web-integrated bioinformatics tools are also provided by tair. for examples, blast, wu-blast, fasta, gbrowse, synteny viewer, seqviewer, motif analysis, and chromosome map tool are powerful for visualization and comparative studies of genes and genome sequence at different scales. […]

2017
PMCID: 5335903
PMID: 28130154
DOI: 10.1016/j.bbagen.2017.01.020

[…] and all mascot identifications were manually verified. amino acid sequence similarity searches were performed against the ncbinr and uniprotkb databases using the blastp program implemented in the wu-blast2 search engine at http://www.bork.embl-heidelberg.de., the relative abundances (expressed as percentage of the total venom proteins) of the different protein families were calculated […]

2017
PMCID: 5507320
PMID: 28644839
DOI: 10.1371/journal.pgen.1006857

[…] determined by ber (http://ber.sourceforge.net). functional domains and gene ontology (go) terms were assigned using interproscan (v. 4.8) []. genes were mapped to kegg orthology (ko) groups using wu-blastp (e < 1e-5). proteins with signal peptides and transmembrane topology were identified using the phobius web server [], and non-classical secretion was predicted using secretomep 1.0 []. […]

2016
PMCID: 4926144
PMID: 27338473
DOI: 10.3390/toxins8060178

[…] hits all mascot identifications were manually verified. amino acid sequence similarity searches were performed against the ncbinr and uniprotkb databases using the blastp program implemented in the wu-blast2 search engine at http://www.bork.embl-heidelberg.de., the relative abundances (expressed as percentage of the total venom proteins) of the different protein families were calculated […]

2016
PMCID: 4949981
PMID: 26948255
DOI: 10.7508/ibj.2016.03.006

[…] two pcr products of each group of healthy individuals as well as hepatitis b and hepatitis c patients were selected randomly and sequenced (takapou zist ltd., iran). the sequences were aligned using wu-blast2 search of the determined sequences against a nucleotide sequence database (embl, european bioinformatics institute). multiple sequence alignments were performed using clustalw in mega5 […]


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WU-BLAST in publications

 (296)
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] snp, transposons, genes, gene families, gene annotations, gene names, proteins, and mutant orderings. multiple web-integrated bioinformatics tools are also provided by tair. for examples, blast, wu-blast, fasta, gbrowse, synteny viewer, seqviewer, motif analysis, and chromosome map tool are powerful for visualization and comparative studies of genes and genome sequence at different scales. […]

PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] in the assembled genome through ab-initio and homology-based methods. for the first method, we applied repeatmodeler_1.0.4 (repeatmodeler, rrid:scr_015027) [] (the parameter set as “–engine_db wublast”) to build a specific repeat database. for the second method, we used known repeat library (repbase) [] to identify repeats with repeatmasker_open-4.0 [] (the parameter set as “-a -nolow […]

PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] sequences were annotated by using censor [] with the repbase ‘vertebrate’ library (downloaded on 1st march, 2016, includes 41,908 sequences). further annotation of consensus sequences was based on wu-blast (v2.0) (https://www.advbiocomp.com/blast/obsolete/) []/ncbi-blast (v2.2.27) [] alignment against a comprehensive retroviral and retrotransposon protein database assembled from the ncbi [], […]

PMCID: 5850084
PMID: 29568489
DOI: 10.5256/f1000research.14771.r31487

[…] in particular when they are nested and degenerated. many software have been developed to detect and annotate tes . one of the best known is repeatmasker, which harnesses nhmmer, cross_match, abblast/wublast, rmblast and decypher as search engines and uses curated libraries of repeats, currently supporting dfam (profile hmm library) and repbase , ., another important tool is the repet package, […]

PMCID: 5764254
PMID: 29324748
DOI: 10.1371/journal.pone.0189524

[…] was < 4, length was < 10 nt or if a transcript contained >10 consecutively repeated bases. transcripts originating from e. coli were also removed from our pool of sequence reads using wu blast. remaining sequence reads were then mapped to known human mirna hairpins using mirbase (v16). alignments were categorized as either exact or loose matches. for loose matches, a custom […]


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WU-BLAST institution(s)
EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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