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

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  McGinnis, Scott ^a   Madden, Thomas L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; INTERNET; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; ONLINE ANALYSIS; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE DATABASE; UNINDEXED SEQUENCE;

DATABASES, GENETIC; GENOME; INTERNET; NUCLEOTIDES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 3242876311     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh435     Document Type: Article

References (13)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Madden,T.L. (2002) The BLAST sequence analysis tool. In McEntyre, J. (ed.), The NCBI Handbook [Internet]. National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD.
4. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214.
5. Ma,B., Tromp,J. and Li,M. (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics, 18, 440-445.
6. Buehler,J. (2001) Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics, 17, 419-428.
7. Marchler-Bauer,A., Panchenko,A.R., Shoemaker,B.A., Thiessen,P.A., Geer,L.Y. and Bryant,S.H. (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
8. Zheng,Z., Schaffer,A.A., Miller,W., Madden,T.L., Lipman,D.J., Koonin,E.V. and Altschul,S.F. (19.98) Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res., 26, 3986-3990.
9. Altschul,S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
10. Chandrasekharappa,S.C., Guru,S.C., Manickam,P., Olufemi,S.E., Collins,F.S., Emmert-Buck,M.R., Debelenko,L.V., Zhuang,Z., Lubensky,I.A., Liotta,L.A. et al. (1997) Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science, 276, 404-407.
11. Pruitt,K.D., Tatusova,T. and Ostell,J. (2002) The Reference Sequence (RefSeq) project. In McEntyre,J. (ed.), The NCBI Handbook [Internet]. National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD.
12. Savan,R. and Sakai,M. (2002) 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. Biochern. Physiol. B Biochem. Mol. Biol., 131, 71-82.
13. Koonin,E.V. (1996) Human choroideremia protein contains a FAD-binding domain. Nature Genet., 12, 237-239.