BLASTX protocols

BLASTX specifications

Information


Unique identifier OMICS_00992
Name BLASTX
Interface Web user interface
Restrictions to use None
Input data Accession numbers, gis, or sequences.
Input format FASTA, TXT
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publications for BLASTX

BLASTX IN pipelines

 (839)
2018
PMCID: 5755334
PMID: 29301488
DOI: 10.1186/s12870-017-1217-x

[…] were clustered using hierarchical clustering. the index to measure the distance was a binary metric., to annotate the reference genes, the sequences of annotated genes were used as queries in the blastx searches against the swiss-prot database, using the blast2go with default parameters [41]. then, gene ontology (go) terms were assigned for annotated genes. enrichment analysis of go […]

2018
PMCID: 5755439
PMID: 29304732
DOI: 10.1186/s12864-017-4421-z

[…] types of all the monokaryotic individuals were determined by the mating tests and confirmed by the genotypes of the flanking markers. predicted gene sequences were analyzed for homology by using blastx with a p value threshold of <10−10. homologs of pheromone precursors were searched among the genome of p. tuoliensis via tblastn of bioedit program [52]. genes and their conserved motifs […]

2018
PMCID: 5758489
PMID: 29313259
DOI: 10.1186/s13568-017-0529-4

[…] sequenced on an illumina hiseq™ 2500 (novogene, beijing, china)., raw reads were cleaned by removing adapter sequences, empty reads, and low quality sequences. for annotation analysis, unigenes were blastx-searched against five databases, namely, the national center for biotechnology information (ncbi) nonredundant (nr) protein sequence database, the ncbi nr nucleotide sequence (nt) database, […]

2018
PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] were calculated. subsequently, the contigs were assembled to construct transcripts with paired-end information and were clustered to obtain unigenes. the assembled unigene sequences were aligned by blastx to publicly available protein databases including the nr (ncbi non-redundant protein), nt, pfam (protein family), cog (clusters of orthologous groups), swissprot, kegg (kyoto encyclopedia […]

2018
PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] family), cog (clusters of orthologous groups), swissprot, kegg (kyoto encyclopedia of genes and genomes) and go (gene ontology) databases. homology searches against the nr database were performed by blastx with a cut-off e-value of 1e-5. unigenes having no homologs in the nr and swissprot databases were scanned using estscan [28]., gene expression levels were estimated by rsem [29]. […]

BLASTX institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

BLASTX review

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Dmitry Magas'

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Web
Useful, but should have better UI