BLASTN protocols

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chevron_left Amino acid sequence homology search Homology-Based Taxonomic Plasmid detection Gene prediction Nucleotide sequence homology search Sequence contamination detection chevron_right
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BLASTN specifications


Unique identifier OMICS_00990
Alternative names Standard Nucleotide BLAST, BLAST, basic local alignment search tool, ncbi 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


  • discontiguous megablast
  • MegaBLAST
  • Rpsblast



  • person_outline Eric W Sayers <>
  • person_outline Alejandro Schaffer <>

Additional information

Publications for Standard Nucleotide BLAST

BLASTN in pipelines

PMCID: 5907373
PMID: 29669586
DOI: 10.1186/s12985-018-0981-z

[…] with an ion 318™ chip v2 and a max read length of 400 bp. the high-quality reads were mapped to the host genomes (anopheles, aedes and culex genomes), and unmapped reads were then classified using blastn and blastx with an e-value cutoff of 1e-03. the virus-related sequences were extracted and assembled with the de novo assembler spades []., extracted rna was used to synthesize cdna using […]

PMCID: 5861454
PMID: 29390076
DOI: 10.1093/nar/gky045

[…] merged using pear v0.9.5 () with a minimum assembly length of 10 bp. the resulted sequences along with unpaired reads were searched against trna sequences of ‘ca. spiroplasma holothuricola’ using blastn alignment (blast+ 2.2.29) with megablast task for sequences longer than 50 bp or with blastn-short task for those shorter than 50 bp, and with an e-value threshold of 1e-5. the fragments […]

PMCID: 5861609
PMID: 29581730
DOI: 10.1186/s13099-018-0239-8

[…] assay was identified by 16s rrna sanger sequencing (genewiz) and the resulting raw data chromatograms were visualized by using the chromas pro software (technolysium ltd.) and then identified with blastn (2.7.1 +) searches []., all samples were dna extracted, amplified, and sequenced by the integrated microbiome resource lab (imr) at dalhousie university (halifax, canada). in brief, dna […]

PMCID: 5818608
PMID: 29459752
DOI: 10.1038/s41598-018-21190-7

[…] reads were assembled using soapdenovo-trans with the following settings: “-k 31 –i 20 -e 3 –m 3 –l 100”. we then searched for matches against a customized virus database (described below) using the basic local alignment search tool (blastn, version 2.2.26), including 6 steps (fig. )., all known viruses in non-redundant nucleotide (nt) databases and their corresponding taxonomic identity […]

PMCID: 5778769
PMID: 29357911
DOI: 10.1186/s13071-017-2561-2

[…] and gfmj01000000). the non-assembled reads were mapped to the rpro genome (rhodnius-prolixus-cdc_scaffolds_rproc3.fa) and proteome (rhodnius-prolixus-cdc_peptides_rproc3.2.fa) using blast (basic local alignment search tool) [] algorithms (blastn and blastx, respectively). non-redundant mapped reads to either database were included as singletons into the assembled dataset […]

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BLASTN in publications

PMCID: 5964351
DOI: 10.1128/mBio.00869-18

[…] de novo contigs were assembled using three programs: codon code aligner, geneious, and dnastar. viral amino acid sequences were created using vector nti. assembled contigs were analyzed using the basic local alignment search tool (blast) from the national center for biotechnology information (ncbi) (). blast searches were conducted at the amino acid level using the protein-protein blast […]

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] 1 and 8,986 reads of library 2). based on this mapping, we performed variant calling and corrected the consensus sequence in cases where the variant was present in more than 85% of the reads., a blastn search revealed two close relatives to our wastewater-associated norovirus genome, norovirus hu/gi.2/jingzhou/2013401/chn (kf306212), which is 7,740 bases in length (), displaying a nucleotide […]

PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] gives results of around 80% ani. we propose the name sarocladium schorii for this organism., antismash analysis suggested the presence of at least 39 secondary metabolite bgc (supplementary fig. ). basic local alignment search tool (blast) searching using the previously identified aspks1 gene rapidly identified a 1.6-mb scaffold as containing a 49-kb bgc potentially involved in tropolone […]

PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] five predicted chia genes. we chose one of these species, the philippine tarsier (t. syrichta), as the reference genome from which to obtain and compare all five chia genes (fig. s1). we blasted (megablast) the t. syrichta gene models against its wgs assembly and confirmed that all five t. syrichta chia sequences map to separate genomic regions (table s1). each of these sequences […]

PMCID: 5955877
PMID: 29769563
DOI: 10.1038/s41598-018-25389-6

[…] eres include bglii_mus, ervb4_1b-ltr_mm, ervb4_3-i_mm, ervb7_1-i_mm, iap1-mm, iapltr3, iapltr3_i, ltris3, orr1a0, rltr10b2, rltr13a3, rltr13b2, rltr13b3, rltr2aiap_mm, rltr4i_mm, and rltr4_mm. a blastn search against all mouse refseq and non-refseq annotated transcripts using these 16 eres showed that the number of expressed loci ranged between 30 and 400, which was considered an adequate […]

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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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