Fast probabilistic analysis of sequence function using scoring matrices

Bioinformatics

Volumn 16, Issue 3, 2000, Pages 233-244

  Wu, Thomas D ^a,c   Nevill Manning, Craig G ^b   Brutlag, Douglas L ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; DATA BASE; PRIORITY JOURNAL; PROBABILITY; SCORING SYSTEM; SEQUENCE ANALYSIS; TECHNIQUE;

EID: 0034046617     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.3.233     Document Type: Article

References (33)

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., Schäffer, 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. Nucl. Acids Res., 25, 3389-3402.
3. Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint database. Prot. Eng., 7, 841-848.
4. Bairoch, A. and Apweiler, R. (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucl. Acids Res., 24, 21-25.
5. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D. and Sonnhammer, E.L.L. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucl. Acids Res., 27, 260-262.
6. 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 Systems in Molecular Biology. AAAI Press, Menlo Park, CA, pp. 47-55.
7. Castillo, E. (1988) Extreme Value Theory in Engineering. Academic Press, Boston.
8. Corpet, F., Gouzy, J. and Kahn, D. (1999) Recent improvements of the ProDom database of protein domain families. Nucl. Acids Res., 27, 263-267.
9. Fuchs, R. (1993) Block searches on VAX and Alpha computer systems. Comput. Appl. Biosci., 9, 587-591.
10. Fuchs, R. (1994) Fast protein block searches. Comput. Appl. Biosci., 10, 79-80.
11. Goldstein, L. and Waterman, M.S. (1994) Approximations to profile score distributions. J. Comput. Biol., 1, 93-104.
12. Gracy, J. and Argos, P. (1998) Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment. Bioinformatics, 14, 164-173.
13. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: Detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
14. Hart, P.E., Nilsson, N.J. and Raphael, B. (1968) A formal basis for the heuristic determination of minimum cost paths. IEEE Trans. Syst. Sci. Cybernet., SSC-4, 100-107.
15. Henikoff, J.G. and Henikoff, S. (1996) Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci., 12, 135-143.
16. Henikoff, S. (1996) Scores for sequence searches and alignments. Curr. Opin. Struct. Biol., 6, 353-360.
17. Henikoff, S. and Henikoff, J.G. (1991) Automated assembly of protein blocks for database searching. Nucl. Acids Res., 19, 6565-6572.
18. Henikoff, S., Henikoff, J.G., Alford, W.J. and Pietrokovski, S. (1995) Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene, 163, GC17-GC26.
19. Henikoff, S., Henikoff, J.G. and Pietrokovski, S. (1999) Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics, 15, 471-479.
20. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wooton, J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
21. McLachlan, A.D. (1983) Analysis of gene duplication repeats in the myosin rod. J. Mol. Biol., 169, 15-30.
22. Nevill-Manning, C., Sethi, K., Wu, T.D. and Brutlag, D.L. (1997) Enumerating and ranking discrete motifs. In Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA, pp. 202-209.
23. Nevill-Manning, C.G., Wu, T.D. and Brutlag, D.L. (1998) Highly specific protein sequence motifs for genome analysis. Proc. Natl Acad. Sci. USA, 95, 5865-5871.
24. Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
25. Pugh, W. (1990) Skip lists: A probabilistic alternative to balanced trees. Commun. ACM, 33, 668-676.
26. Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A. and Haussier, D. (1996) Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
27. Smith, H.O., Annau, T.M. and Chandrasegaran, S. (1990) Finding sequence motifs in groups of functionally related proteins. Proc. Natl Acad. Sci. USA, 87, 826-230.
28. Staden, R. (1989) Methods for calculating the probabilities of finding patterns in sequences. Comput. Applic. Biosci., 5, 89-96.
29. Staden, R. (1990) Searching for patterns in protein and nucleic acid sequences. Meth. Enzymol., 183, 193-211.
30. Stormo, G.D. and Hartzell III, G.W. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
31. 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.
32. Wallace, J.C. and Henikoff, S. (1992) PATMAT: A searching and extraction program for sequence, pattern and block queries and databases. Comput. Appl. Biosci., 8, 249-254.
33. Wu, T.D., Nevill-Manning, C.C. and Brutlag, D.L. (1999) Minimalrisk scoring matrices for sequence analysis. J. Comput. Biol., 6. 219-235.