MegaBLAST protocols

MegaBLAST specifications

Information


Unique identifier OMICS_01435
Name MegaBLAST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alejandro Schaffer <>

Additional information


https://gordonlab.wustl.edu/btheta/blast/docs/megablast_readme.html

Publication for MegaBLAST

MegaBLAST IN pipelines

 (119)
2018
PMCID: 5764372
PMID: 29324824
DOI: 10.1371/journal.pone.0191183

[…] (biomatters inc., auckland, new zealand). gene alignments were exported as fasta files for subsequent analyses. sequences are deposited in genbank under accession numbers ky856727-ky856739., we used megablast to compare 18s sequences from collected nematodes to all nucleotide sequences available in genbank. we used top blast hits together with evidence from the literature on nematodes […]

2018
PMCID: 5834208
PMID: 29462150
DOI: 10.1371/journal.pntd.0006185

[…] industries (pty) ltd (pretoria, south africa)., the obtained plant dna sequences for each gene were cleaned, edited and compared to reference sequences in the genbank database [47]. in genbank, the ‘megablast’ search option of nucleotide basic local alignment search tool (blastn) [48] algorithm was used with the default search parameters. the hits with sequence identity above 96% were retrieved […]

2018
PMCID: 5878103
PMID: 29623245
DOI: 10.1371/currents.outbreaks.7d65e5eb6ef75664da68905c5582f7f7

[…] mutation (transversion: t / a) in position 386 related to the orov reference sequence for segment s nc_005777., we also conducted a blast analysis 9 over the consensus nucleotide sequence, using the megablast algorithm 10. only orthobunyavirus sequences were retrieved among the first 100 hits with the higher score and lower e-values. the closest nucleotide sequence returned from the megablast […]

2018
PMCID: 5878103
PMID: 29623245
DOI: 10.1371/currents.outbreaks.7d65e5eb6ef75664da68905c5582f7f7

[…] using the megablast algorithm 10. only orthobunyavirus sequences were retrieved among the first 100 hits with the higher score and lower e-values. the closest nucleotide sequence returned from the megablast analysis belongs to an oropouche virus isolated in peru 2008 (strain tvp-19256/iqe-7894 - kp795086) sharing 98% similarity, with 545/558 identical sites., recently, the international […]

2018
PMCID: 5880176
PMID: 29610707
DOI: 10.7717/peerj.4560

[…] observed between the automatic annotation and pan-genome comparison were corrected based on the results of the aforementioned work when feasible., the second method was based on blasting (blastn megablast, ncbi database) relevant staphylococcus reference sequences, retrieved from genbank and originating from reviewed protein sequences in uniprot, against the whole genome sequences […]

MegaBLAST institution(s)
National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Rockville Pike, Bethesda, MD, USA
MegaBLAST funding source(s)
Supported by Intramural Research Program of the National Institutes of Health, NLM.

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