Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

Journal of Molecular Biology

Volumn 284, Issue 4, 1998, Pages 1201-1210

  Park, Jong ^a,e   Karplus, Kevin ^b   Barrett, Christian ^b   Hughey, Richard ^b   Haussler, David ^b,c   Hubbard, Tim ^d   Chothia, Cyrus ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b University of California Santa Cruz   (United States)

^c ISAAC NEWTON INSTITUTE FOR MATHEMATICAL SCIENCES   (United Kingdom)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Hidden Markov models; Intermediate sequence search; Protein homology; PSI BLAST; SAM T98; SCOP

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ERROR; METHODOLOGY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0032509105     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2221     Document Type: Article

References (26)

1. Altschul S. F., Gish W. Local alignment statistics. Methods Enzymol. 266:1996;460-480.
2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
3. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acid Res. 25:1997;3389-3402.
4. Baldi P., Chauvin Y., Hunkapiller T., McClure M. A. Hidden Markov models of biological primary sequence information. Proc. Natl Acad. Sci. USA. 91:1994;1059-1063.
5. Bashford D., Chothia C., Lesk A. M. Determinants of a protein fold: unique features of the globin amino acid sequences. J. Mol. Biol. 196:1987;199-216.
6. Brenner S. E., Chothia C., Hubbard T. Assessment of sequence comparison methods with reliable structurally-identified distant evolutionary relationships. Proc. Natl Acad Sci. USA. 95:1998;6073-6078.
7. Eddy S. R. ISMB 95, Intelligent Systems in Molecular Biology(Conference),Multiple Alignment Using Hidden Markov Models. 1995.
8. Eddy S. R. Hidden Markov models. Curr. Opin. Struct. Biol. 6:1996;361-365.
9. Eddy S. R., Mitchison G., Durbin R. Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol. 2:1995;9-23.
10. Gribskov M., McLachlan A. D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA. 84:1987;4355-4358.
11. Holm L., Sander C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics. 14:1998;423-429.
12. Hughey R., Krogh A. Hidden Markov models for sequence analysis: Extension and analysis of the basic method. CABIOS. 12:1996;95-107.
13. Karplus K., Sjolander S., Barrett C., Cline M., Haussler D., Hughey R., Holm L., Sander C. Predicting protein structure using hidden Markov models. Proteins: Struct. Funct. Genet. 1:1997;134-139 (Suppl.).
14. Karplus K., Barrett C., Hughey R. Fold Recognition by Remote Homology Detection Using Hidden Markov Models,Technical Report UCSC-CRL-98-06, Department of Computer Science, University of California at Santa Cruz, CA 95064. Obtain able at ftp://ftp.cse.ucsc.edu/pub/tr/ucsc-crl-98-06. ps.Z. 1998.
15. Krogh A., Brown M., Mian I. S., Sjolander K., Haussler D. Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235:1994;1501-1531.
16. Luthy R., Xenarios I., Bucher P. Improving the sensitivity of the sequence of the sequence profile method. Protein Sci. 3:1994;139-146.
17. Murzin A. G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:1998;380-387.
18. Murzin A. G., Brenner S. E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
19. Neuwald A., Liu J., Lipman D., Lawrence C. Extracting protein alignment models from the sequence database. Nucl. Acids Res. 25:1997;1665-1667.
20. Park J., Teichmann S. A., Hubbard T., Chothia C. Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 273:1997;249-254.
21. Pearson W. R. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
22. Sjolander K., Karplus K., Brown M., Hughey R., Krogh A., Mian S., Haussler D. Dirichlet mixtures: a method for improving detection of weak but significant protein sequence homology. CABIOS. 12:1996;327-345.
23. Tatusov R. L., Altschul S. F., Koonin E. V. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA. 91:1994;12091-12095.
24. Taylor W. R. Identification of protein sequence homology by consensus template alignment. J. Mol. Biol. 188:1986;233-258.
25. Thompson J. D., Higgins D. G., Gibson T. J. Improved sensitivity of profile searches through the use of sequence weights and gap excision. CABIOS. 10:1994;19-29.
26. Yi T. M., Lander E. S. Recognition of related proteins by iterative template refinement (ITR). Protein Sci. 3:1994;1315-1328.