BLASTX protocols

View BLASTX computational protocol

BLASTX statistics

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Popular tool citations

chevron_left Metabolic network analysis Read alignment Gene Ontology annotation Gene orthology prediction Nucleotide sequence homology search Protein database search Gene prediction chevron_right
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Associated diseases

Associated diseases

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

 (1803)
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 []. 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 []. 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: 5766536
PMID: 29330451
DOI: 10.1038/s41598-017-16399-x

[…] of uninterrupted orfs. the workflow was identical to the one employed for the initial search until obtaining the set of extended hit loci. these were directly compared to the diverse library using blastx with default parameters (except −e = 1e−5). queries with a best alignment score against any member of the caulimoviridae with an alignment length above 80% of subject length (set generically […]


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BLASTX in publications

 (6716)
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] present in each sample was assessed by comparison of curated read and contig data sets with both the refseq viral protein database and the nonredundant protein database of ncbi, using diamond blastx () and lowest-common-ancestor taxon assignment with megan6 (). for wastewater samples li_13-9, le_13-9, and le_11-10, two libraries were processed (indicated with _1 and _2 in the data set […]

PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] strains (fig. ). in genomes a, b, d and g no genes were predicted in the region where mat1–2 gene was expected. when this region was manually searched against the genbank database for proteins with blastx, no matches were found. however, when these genomic regions were compared to the well-conserved mat1–2 genes from other h. werneckii strains, the similarity was clearly recognizable, […]

PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] trinity [] software was used to assemble all clean high-quality reads. the expression level of transcripts was measured by rsem, and the result was reported by units of tpm (transcripts per million).blastx was employed to annotate the function of unigene sequences using no redundant (nr) protein database (ncbi), swiss prot database, kegg (kyoto encyclopedia of genes and genomes), cog (clusters […]

PMCID: 5952423
PMID: 29764461
DOI: 10.1186/s12985-018-0998-3

[…] subsequent sanger sequencing., illumina nextseq sequencing was applied to total rnas prepared from three diseased apple trees. sequence reads were de novo assembled, and contigs were annotated by blastx. rt-pcr and 5′/3’ race sequencing were used to obtain the complete genome of a new virus. rt-pcr was used to detect the virus., three common apple viruses and a new luteovirus were identified […]

PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] cleaned reads were de novo assembled using an in-house sequence assembler employing an ensemble strategy (), and the resulting assembled contigs were compared to the genbank protein database using blastx. once the viral contigs were identified, a complete circular genome was constructed from the available contigs and reads using geneious (biomatters), which was also used to generate coverage […]


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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