BLASTN pipeline

BLASTN specifications

Information


Unique identifier OMICS_00990
Name BLASTN
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

Subtools


  • discontiguous megablast
  • MegaBLAST
  • RPS-BLAST
  • Rpsblast

Documentation


Maintainer


  • person_outline Eric W Sayers <>

Additional information


https://www.ncbi.nlm.nih.gov/books/NBK279690/

Publications for Standard Nucleotide BLAST

BLASTN citations

 (446)
2018
PMCID: 5722268

[…] content (%)., l0-3 and l0-4 drafts genomes (genbank accession numbers lihe00000000 and liiy00000000) present ~4.2 and 4.3 mb for chromosome i and ~400 and 422 kb for chromosome ii, respectively. blastn against nonredundant ncbi database was applied for the remaining contigs, that did not align with the reference, and resulted in high identity with chinese serovar canicola published plasmids […]

2018
PMCID: 5785972

[…] were monitored by increasing temperature from 25 to 90 °c. melting temperatures were determined from the first derivative curve., iterative searching for petase-like proteins was performed by basic local alignment search tool (blast) in national center for biotechnology information (ncbi) server using position-specific iterated blast (psi-blast) method. multiple alignment was performed […]

2018
PMCID: 5793084

[…] pcr products (5 μl) were detected by 0.1% agar gel electrophoresis at 120 v for 30 min and were submitted for sequencing. the sequencing results were compared with sequences from genbank using the basic local alignment search tool (https://blast.ncbi.nlm.nih.gov/blast.cgi)., sequences of the marine-derived fungal its-rdna regions were compared with related sequences from the ncbi […]

2018
PMCID: 5802912

[…] were compared with sequences of other ppn species, obtained by searching the genbank nucleotide database (http://www.ncbi.nlm.nih.gov) using the software bioedit; and similarity was evaluated using blastn 2.2.19+ program [27]., phylogenetic analyses were conducted in mega 6 [28]. hasegawa-kishino-yano model [29] showed the lowest bic scores (bayesian information criterion) and was considered […]

2018
PMCID: 5826968

[…] represent average enrichment for three biological replicates., orthologous groups were identified using orthofinder (emms and kelly, 2015), by which all nucleotide sequences were compared using a blastn all-against-all search with an e-value cutoff of <10-4. nucleotide sequences used to construct the phylogenetic tree were aligned in mafft (katoh and standley, 2013), and a maximum […]

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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