BLASTN protocols

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BLASTN computational protocol

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 IN pipelines

 (1071)
2018
PMCID: 5722268
PMID: 29236931
DOI: 10.1590/0074-02760170119

[…] 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: 5752868
PMID: 29101189
DOI: 10.1128/AEM.01712-17

[…] using bioedit 7.0.0 software (78), followed by the determination of their relatedness to type reference strain sequences in the genbank database (https://www.ncbi.nlm.nih.gov/genbank/) using the blastn program. each isolate sequence was aligned with type reference strain (genbank database) using muscle (79). phylogenetic trees were generated from the aligned sequences using the mega 6 […]

2018
PMCID: 5756416
PMID: 29304740
DOI: 10.1186/s12864-017-4301-6

[…] over each of the 10 rrna operons was verified by identification of pacbio reads, which completely traverse each of them. unique sequences (350 bp) on either side of each operon were used for blastn against the set of pacbio reads. a total of 370 pacbio reads traversed rrna operons completely, having matches to upstream as well as downstream unique sequences (as revealed by a custom perl […]

2018
PMCID: 5766633
PMID: 29330501
DOI: 10.1038/s41598-017-18934-2

[…] ltr regions using sanger sequencing data. short servs (<~2 kb; svl id; 13c, 15f, 22e, 26) were sequenced by the sanger method. the sequences of primers are listed in supplementary table s4. a blastn homology search50 was performed for serv sequences; aligned images of homologous regions were visualized with the gview server (https://server.gview.ca/)55 and act program56. in order […]

2018
PMCID: 5769438
PMID: 29335005
DOI: 10.1186/s40168-017-0387-y

[…] for metagenomic sequences. quality assemblies’ quantification was performed by quast software [48]. predicted genes were first annotated against the rescap database by best blast hit approach using blastn software [49]. to identify only the genes belonging to the rescap database or their homologs and to minimize the false positive ratio, blast hits were filtered by e value of 10−100 and 80% […]

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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