The complexity of the dirichlet model for multiple alignment data

Journal of Computational Biology

Volumn 18, Issue 8, 2011, Pages 925-939

  Yu, Yi Kuo ^a   Altschul, Stephen F ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

alignment; computational molecular biology; dynamic programming; multiple alignment; sequence analysis

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; METHODOLOGY; MONTE CARLO METHOD; PROBABILITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, STATISTICAL; MONTE CARLO METHOD; PROBABILITY; PROTEINS; SEQUENCE ALIGNMENT;

EID: 79961161809     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0039     Document Type: Article

References (7)

1. Altschul, S.F., Gertz, E.M., Agarwala, R., et al. 2009. PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res. 37, 815-824.
2. Altschul, S.F., Wootton, J.C., Zaslavsky, E., et al. 2010. The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comp. Biol. 6, e1000852.
3. Brown, M., Hughey, R., Krogh, A., et al. 1993. Using Dirichlet mixture priors to derive hidden Markov models for protein families, 47-55. In Hunter, L., Searls, D., and Shavlik, J., eds. Proc. First Int. Conf. on Intelligent System for Mol. Biol. AAAI Press, Menlo Park, CA.
4. Grünwald, P.D. 2007. The Minimum Description Length Principle. MIT Press, Cambridge, MA.
5. Marsaglia, G. 1972. Choosing a point from the surface of a sphere. Ann. Math. Stat. 43, 645-646.
6. Sjölander, K., Karplus, K., Brown, M., et al. 1996. Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12, 327-345. (Pubitemid 26345169)
7. Ye, X., Yu, Y.-K., and Altschul, S.F. 2011. On the inference of Dirichlet mixture priors for protein sequence comparison. J. Comput. Biol. 18 (this issue).