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Protocols

BLASTN specifications

Information


Unique identifier OMICS_00990
Name BLASTN
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

Subtools


  • discontiguous megablast
  • MegaBLAST
  • RPS-BLAST
  • Rpsblast

Documentation


Maintainers


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

Additional information


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

Publications for Standard Nucleotide BLAST

BLASTN citations

 (16987)
library_books

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

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

call_split

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

2018
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x
call_split See protocol

[…] western blots are shown in supplementary fig. .  all bacterial expression experiments were performed in duplicate., sequence comparisons to the sea urchin genome were done using blast, blastp, or blastn at https://blast.ncbi.nlm.nih.gov/blast.cgi or www.echinobase.org using either standard parameters or with low complexity filter turned off. multiple sequence alignments were performed using […]

library_books

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

2018
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 […]

library_books

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription qPCR data in mice

2018
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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