PCMA: Fast and accurate multiple sequence alignment based on profile consistency

Bioinformatics

Volumn 19, Issue 3, 2003, Pages 427-428

  Pei, Jimin ^a   Sadreyev, Ruslan ^a   Grishin, Nick V ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; INTERMETHOD COMPARISON; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 0037433034     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg008     Document Type: Article

References (8)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,Z. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Bahr,A., Thompson,J.D., Thierry,J.C. and Poch,O. (2001) BA1-iBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29, 323-326.
3. Huang,X.Q. and Miller,W. (1991) A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math., 12, 337-357.
4. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
5. Pearson,W.R. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 276, 71-84.
6. Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
7. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
8. Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.