Refining multiple sequence alignments with conserved core regions

Nucleic Acids Research

Volumn 34, Issue 9, 2006, Pages 2598-2606

  Chakrabarti, Saikat ^a   Lanczycki, Christopher J ^a   Panchenko, Anna R ^a   Przytycka, Teresa M ^a   Thiessen, Paul A ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; ARTICLE; BIOLOGY; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC CONSERVATION; INTERNET; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; QUALITY CONTROL; SCORING SYSTEM; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; ALGORITHM; AMINO ACID SEQUENCE; COMPARATIVE STUDY; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; STANDARD; VALIDATION STUDY;

ALGORITHMS; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; INTERNET; MOLECULAR SEQUENCE DATA; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 33646912732     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl274     Document Type: Article

References (26)

1. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. et al. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
2. Servant,F., Bru,C., Carrere,S., Courcelle,E., Gouzy,J., Peyruc,D. and Kahn,D (2002) ProDom: Automated clustering of homologous domains. Brief. Bioinformatics, 3, 246-251.
3. Letunic,I., Goodstadt,L., Dickens,N.J., Doerks,T., Schultz,J., Mott,R., Ciccarelli,F., Copley,R.R., Ponting,C.P. and Bork,P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242-244.
4. 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.
5. Lipman,D.J., Altschul,S.F. and Kececioglu,J.D. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
6. Stoye,J., Moulton,V. and Dress,A.W. (1997) DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Comput Appl Biosci., 13, 625-626.
7. Hogeweg,P. and Hesper,B. (1984) The alignment of sets of sequences and the construction of phyletic trees: An integrated method. J. Mol. Evol., 20, 175-186.
8. Feng,D.F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-360.
9. Taylor,W.R (1988) A flexible method to align large numbers of biologicalsequences. J. Mol. Evol., 28, 161-169.
10. 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.
11. Barton,G.J. and Sternberg,J.E. (1987) A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J. Mol. Biol., 198, 327-337.
12. Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
13. Notredame,C. and Higgins,D.G. (1996) SAGA: Sequence alignment by genetic algorithm. Nucl. Acids Res., 24, 1515-1524.
14. Heringa,J. (2002) Local weighting schemes for protein multiple sequence alignment. Comput. Chem., 26, 459-477.
15. Berger,M.P. and Munson,P.J. (1991) A novel randomized iterative strategy for aligning multiple protein sequences. Comput. Appl. Biosci., 7, 479-484.
16. Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
17. Do,C.B., Mahabhashyam,M.S., Brudno,M. and Batzoglou,S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 2, 330-340.
18. Wang,Y. and Li,K.B. (2004) An adaptive and iterative algorithm for refining multiple sequence alignment. Comput. Biol. Chem., 28, 141-148.
19. Wallace,I.M., O'Sullivan,O. and Higgins,D.G (2005) Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics, 21, 1408-1414.
20. 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.
21. Madej,T., Gibrat,J-F. and Bryant,S.H. (1995) Threading a database of protein cores. Protein Struct. Funct. Genet., 23, 356-369.
22. Gibrat,J.F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
23. Chen,J., Anderson,J.B., DeWeese-Scott,C., Fedorova,N.D., Geer,L.Y., He,S., Hurwitz,D.I., Jackson,J.D., Jacobs,A.R., Lanczycki,C.J. et al. (2003) MMDB: Entrez's 3D-structure database. Nucleic Acids Res., 31, 474-477.
24. Kann,M.G., Thiessen,P.A., Panchenko,A.R., Schaffer,A.A., Altschul,S.F. and Bryant,S.H. (2005) A structure-based method for protein sequence alignment. Bioinformatics, 21, 1451-1456.
25. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
26. Panchenko,A.R., Kondrashov,F. and Bryant,S. (2004) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci., 13, 884-892.