PSI-BLAST pseudocounts and the minimum description length principle

Nucleic Acids Research

Volumn 37, Issue 3, 2009, Pages 815-824

  Altschul, Stephen F ^a   Gertz, E Michael ^a   Agarwala, Richa ^a   Schäffer, Alejandro A ^a   Yu, Yi Kuo ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; ENTROPY; GENETIC CONSERVATION; INFORMATION RETRIEVAL; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; METHODOLOGY;

DATABASES, PROTEIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 63349085642     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn981     Document Type: Article

References (35)

1. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
2. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
3. Altschul,S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
4. Dayhoff,M.O., Schwartz,R.M. and Orcutt,B.C. (1978) A model of evolutionary change in proteins. In Dayhoff,M.O. (ed.), Atlas of Protein Sequence and Structure, Vol. 5, National Biomedical Research Foundation, Washington, DC, pp. 345-352.
5. Schwartz,R.M. and Dayhoff,M.O. (1978) Matrices for detecting distant relationships. In Dayhoff,M.O. (ed.), Atlas of Protein Sequence and Structure, Vol. 5, National Biomedical Research Foundation, Washington, DC, pp. 353-358.
6. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
7. Altschul,S.F., Carroll,R.J. and Lipman,D.J. (1989) Weights for data related by a tree. J. Mol. Biol., 207, 647-653.
8. Sibbald,P.R. and Argos,P. (1990) Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol. 216, 813-818.
9. Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Protein Struct. Funct. Genet., 9, 56-68.
10. Gerstein,M., Sonnhammer,R. and Clothia,C. (1994) Volume changes in protein evolution. J. Mol. Biol., 236, 1067-1078. (Appendix: A method to weight protein sequences to correct for unequal representation.).
11. Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
12. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci., 10, 19-29.
13. Eddy,S.R., Mitchison,G. and Durbin,R. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2 9-23.
14. Gotoh,O. (1995) A weighting system and algorithm for aligning many phylogenetically related sequences. Comput. Appl. Biosci., 11 543-551.
15. Krogh,A. and Mitchison,G. (1995) Maximum entropy weighting of aligned sequences of protein or DNA. In Rawlings,C., Clark,D., Altman,R., Hunter,L., Lengauer,T. and Wodak,S. (eds), Proceedings of the Third International Conference on Intelligent system for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 215-221.
16. Bailey,T.L. and Gribskov,M. (1996) The megaprior heuristic for discovering protein sequence patterns. In States,D.J., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R. (eds), Proceedings of the Fourth International Conference on Intelligent system for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 15-24.
17. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
18. Schäffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
19. Brown,M., Hughey,R., Krogh,A., Mian,I.S., Sjölander,K. and Haussler,D. (1993) Using Dirichlet mixture priors to derive hidden Markov models for protein families. In Hunter,L., Searls,D. and Shavlik,J. (eds), Proceedings of the First International Conference on Intelligent system for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 47-55.
20. Sjölander,K., Karplus,K., Brown,M., Hughey,R., Krogh,A., Mian,I.S. and Haussler,D. (1996) Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
21. Tatusov,R.L., Altschul,S.F. and Koonin,E.V. (1994) Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA, 91, 12091-12095.
22. Henikoff,J.G. and Henikoff,S. (1996) Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci., 12, 135-143.
23. Grünwald,P.D. (2007) The Minimum Description Length Principle, MIT Press, Cambridge, MA.
24. Chandonia,J.-M., Hon,G., Walker,N.S., Lo Conte,L., Koehl,P., Levitt,M. and Brenner,S.E. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, D189-D192.
25. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
26. Brenner,S.E., Chothia,C. and Hubbard,T.J. (1998) Assessing sequence comparison methods with reliable structurally identified-distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
27. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R. and Federhen,S. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 36, D13-D21.
28. Gribskov,M. and Robinson,N.L. (1996) Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-33.
29. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
30. Grünwald,P.D. (2005) Minimum description length tutorial. In Grünwald,P.D., Myung,I.J. and Pitt,M.A. (eds), Advances in Minimum Description Length: Theory and Applications, MIT Press Cambridge, MA, pp. 23-79.
31. Cover,T.M. and Thomas,J.A. (1991) Elements of Information Theory, Wiley, New York.
32. Fisher,R.A. (1925) Theory of statistical estimation. Proc. Cambridge Phil. Soc., 22, 700-725.
33. Schäffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000-1011.
34. Boeckmann,B., Bairoch,A., Apweiller,R., Blatter,M.-C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
35. Nishida,K., Frith,M.C. and Nakai,K. (2008) Pseudocounts for transcription factor binding sites. Nucleic Acids Res. (in press).