BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Nucleic acids research ·Vol. 32 ·No. Web Server issue ·2004-07-01 ·Pages W20-5

McGinnis S, Madden TL

Abstract

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.

MeSH Terms

Databases, Genetic Genome Internet Nucleotides/chemistry Sequence Alignment Sequence Analysis Sequence Analysis, Protein Software User-Computer Interface

Chemicals

Nucleotides

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

McGinnis Scott

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA. mcginnis@ncbi.nlm.nih.gov

Madden Thomas L

References (11)

11 references, click to expand

A greedy algorithm for aligning DNA sequences.
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14 PMID: 10890397
Efficient large-scale sequence comparison by locality-sensitive hashing.
Bioinformatics. 2001 May;17(5):419-28 PMID: 11331236
Analysis of expressed sequence tags (EST) obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A.
Comp Biochem Physiol B Biochem Mol Biol. 2002 Jan;131(1):71-82 PMID: 11742760
CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
Nucleic Acids Res. 2002 Jan 1;30(1):281-3 PMID: 11752315
PatternHunter: faster and more sensitive homology search.
Bioinformatics. 2002 Mar;18(3):440-5 PMID: 11934743
Protein sequence similarity searches using patterns as seeds.
Nucleic Acids Res. 1998 Sep 1;26(17):3986-90 PMID: 9705509
Amino acid substitution matrices from an information theoretic perspective.
J Mol Biol. 1991 Jun 5;219(3):555-65 PMID: 2051488
Human choroideremia protein contains a FAD-binding domain.
Nat Genet. 1996 Mar;12(3):237-9 PMID: 8589712
Positional cloning of the gene for multiple endocrine neoplasia-type 1.
Science. 1997 Apr 18;276(5311):404-7 PMID: 9103196
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
Basic local alignment search tool.
J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkh435

mcginnis@ncbi.nlm.nih.gov

Published

2004-07-01

Pages

W20-5

Language

English

Region

England

NLM ID

0411011

PMCID

PMC441573

Subset

External Links

PubMed source DOI: 10.1093/nar/gkh435 PMC Full Text View journal details

Analysis Services

BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Contact

WeChat Official Account