WU-BLAST pipeline

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

 (15)
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) [84]. 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 [85], and non-classical secretion was predicted using secretomep 1.0 […]

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 […]

2012
PMCID: 3368713
PMID: 22475018
DOI: 10.1186/1471-2164-13-129

[…] study are available from gdr http://www.rosaceae.org/bmc_rosaceae_genome_paper. the whole genome sequences of peach and grape were masked for repeats using repeatmasker [39], as well as the nmerge, wu-blast distribution, and fasoftmask distribution utilities of mercator [25]. mercator identifies orthologous regions with one to one ortholgy relationships, rather than producing any syntenic […]

2011
PMCID: 3040727
PMID: 21266071
DOI: 10.1186/1471-2164-12-60

[…] proteins, and protein domains. to control for these issues we performed a simulation to help us determine the best e-value threshold for a conopeptide hits in rna-seq data. we first ran wu-blastp [36] on our transcriptome assembly against the combined database of uniprotkb [40] and conopeptides from conoserver [42]. in total, 6,677 peptides were found to have a known conopeptide […]

2011
PMCID: 3138424
PMID: 21546564
DOI: 10.1093/gbe/evr037

[…] and lipman 1988; pearson et al. 1997). regions of the genome sequence containing nonoverlapping repeated elements were mapped with repeatmasker (http://www.repeatmasker.org/) running under the wu-blast 2.0 search engine (http://blast.wustl.edu/), using the repeats ≥30 bp identified with repfind of the reputer 2.74 program (kurtz et al. 2001) as input sequences., the sidedness index (cs) […]

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

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