BLASTN pipeline

BLASTN specifications


Unique identifier OMICS_00990
Alternative names Standard Nucleotide BLAST, BLAST, Basic Local Alignment Search Tool, blastall, blast+
Interface Web user interface
Restrictions to use None
Input data Some accession number(s) or sequence(s).
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes


  • MegaBLAST
  • discontiguous megablast
  • Rpsblast



  • person_outline Eric W Sayers <>

Additional information

Publications for Standard Nucleotide BLAST

BLASTN citations

PMCID: 5951914

[…] using trnascan-se41, with introns removed by our own python code. in some kluyveromyces species, the tlcag gene was not predicted by trnascan-se due to its unusually long intron but was found by blastn. in our phylogenetic trees, trnas are identified with names such as s_cag1_ser1_babino_r2_i_25. the fields (separated by underscores) in these names are: inferred amino acid; anticodon; clade; […]

PMCID: 5942804

[…] by zhang et al. [45]. novel st and vt assignments are available at the website for each typing database [44, 46]. presence of pathogenicity islands and virulence genes [9, 47] were identified using blastn with e values set to a minimum of 1x10-30, a minimum percent identity set to 90%, and a minimum query coverage of 80%. differences in the proportions of virulence factors and pathogenicity […]

PMCID: 5934491

[…] and manually refined. operational taxonomic units (otus) were identified using a sequence identity threshold of 97% (0.03) using mothur (v.1.39.5) (schloss et al., 2009). taxonomy was assigned using blastn (altschul et al., 1997) and arb (ludwig et al., 2004). for phylogenetic analyses of sequences affiliated with chlorobi and δ-proteobacteria, the top blast matches and nearest relative […]

PMCID: 5915607

[…] contigs with a total length of 1,340,105 bp were assembled including 12 circles (ranging from 13.5 to 120.6 kb) and 7 single lines (837,015 bp)., the assembled contigs were firstly annotated by ncbi-blastn based on the local database with an e-value < 1e−6. then, the boundaries of each gene were confirmed by mitofy and exported as sequin formatted files. trna genes were further predicted […]

PMCID: 5914023

[…] with isotigs of each library. because reads were mapped, for example using the bwa software package [64], when only portions of ests showed high similarity, we selected a broader comparison by the blastn algorithm with default parameters, using reference sequences as queries and isotigs of each library as subjects. we regarded a reference sequence as expressed in an organ if the sequence […]

BLASTN institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
BLASTN funding source(s)
This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.

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