Score distributions for simultaneous matching to multiple motifs

Journal of Computational Biology

Volumn 4, Issue 1, 1997, Pages 45-59

  Bailey, Timothy L ^a   Gribskov, Michael ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

extreme value distributions; profiles; protein motifs; score normalization; score p values; sum statistics

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0030965735     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1997.4.45     Document Type: Article

References (19)

1. Altschul, S.F., and Gish, W. 1996. Local alignment statistics. Methods Enzymol. 266, 460-480.
2. 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.
3. Bailey, T.L., and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
4. Bailey, T.L., and Elkan, C. 1995. Unsupervised learning of multiple motifs in biopolymers using EM. Machine Learning 21, 51-80.
5. Bairoch, A. 1994. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res. 22, 3578-3580.
6. Bairoch, A. 1995. The PROSITE database, its status in 1995. Nucleic Acids Res. 24, 189-196.
7. Goldstein, L., and Waterman, M.S. 1994. Approximations to profile score distributions. J. Comput. Biol. 1, 93-104.
8. Gribskov, M., and Robinson, N.L. 1996. The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20, 25-33.
9. Gribskov, M., Lüthy, R., and Eisenberg, D. 1990. Profile analysis. Methods Enzymol. 183, 146-159.
10. Hall, P. 1980. Estimating probabilities for normal extremes. Adv. Appl. Prob. 12, 491-500.
11. Henikoff, S., and Henikoff, J.G. 1991. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19, 6565-6572.
12. Kinnison, R.R. 1985. Applied Extreme Value Statistics. Battelle Press, Richland, Washington.
13. Krogh, A., Brown, M., Mian, I.S., Sjölander, K., and Haussler, D. 1994. Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol. 235, 1501-1531.
14. 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.
15. Pearson, W.R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63-98.
16. Pietrokovski, S., Henikoff, S., and Henikoff, J.G. 1996. The BLOCKS database - a system for protein classification. Nucleic Acids Res. 24, 197-200.
17. Press, W.H., Flannery, B.P., Teukolsky, S.A., and Vetterling, W.T. 1986. Numerical Recipes. Cambridge University Press, Cambridge, England.
18. Smith, T., and Waterman, M. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
19. Stormo, G.D. 1990. Consensus patterns in DNA. Methods Enzymol. 183, 211-221.