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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 citations


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] rm. 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 (blast […]


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] 1 and the options --careful and a minimum coverage of 5 reads per contig (). The contig files of each sample were compared with the contigs of the controls (assembled using the same parameters) using blastn of the BLAST+ suite (). Contigs that showed significant similarity with control contigs were manually removed, creating a curated contig data set. The unmapped read data sets were then mapped a […]


Identification and tissue distribution of chemosensory protein and odorant binding protein genes in Tropidothorax elegans Distant (Hemiptera: Lygaeidae)

Sci Rep
PMCID: 5958050
PMID: 29773848
DOI: 10.1038/s41598-018-26137-6

[…] Signal peptides were predicted using SignalP 4.1 server ( The similarity searches were performed using NCBI BLAST ( Multiple sequence alignment was conducted using DNAMAN 6.0. Amino acid sequence alignments of the matured OBPs and CSPs from T. elegans and other Hemiptera […]


Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A

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

[…] ies 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 biosynt […]


AID/APOBEC like cytidine deaminases are ancient innate immune mediators in invertebrates

Nat Commun
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] Sequence comparisons to the sea urchin genome were done using BLAST, BLASTP, or BLASTN at or using either standard parameters or with low complexity filter turned off. Multiple sequence alignments were performed using CL […]


Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

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

[…] us rotundus) three or more CHIAs in their genomes (tables S1 and S3). These libraries have been deposited into NCBI’s Sequence Read Archive, so we queried them via NCBI’s BLAST interface. We BLASTed (megablast) all five of the assembled T. chinensis CHIA paralogs against a pancreas library (). M. californicus and D. rotundus are phyllostomid chiropterans with no available genome assemblies, so we […]


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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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