A probabilistic model for sequence alignment with context-sensitive indels

Journal of Computational Biology

Volumn 18, Issue 11, 2011, Pages 1449-1464

  Hickey, Glenn ^a   Blanchette, Mathieu ^b  

^a University of California Santa Cruz   (United States)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

algorithms; molecular evolution; sequence analysis

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC ASSOCIATION; HUMAN; HUMAN GENOME; INDEL MUTATION; METHODOLOGY; PROBABILITY; SEQUENCE ALIGNMENT; STANDARD; STATISTICAL MODEL;

ALGORITHMS; BAYES THEOREM; COMPUTER SIMULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INDEL MUTATION; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; REFERENCE STANDARDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 80955139627     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0157     Document Type: Article

References (36)

1. Ball, E., Stenson, P., Abeysinghe, S., et al. 2005. Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum. Mutat. 26, 205-213. (Pubitemid 41254376)
2. Benson, G. 1997. Sequence alignment with tandem duplication. J. Comput. Biol. 4, 351-367. (Pubitemid 27355873)
3. Bérard, S., and Rivals, E. 2003. Comparison of minisatellites. J. Comput. Biol. 10, 357-372. (Pubitemid 37372154)
4. * 1. J. Mol. Biol. 190, 159-165. (Pubitemid 16032944)
5. Chen, F., Chen, C., Li, W., et al. 2007. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res. 17, 16.
6. Chuzhanova, N., Anassis, E., Ball, E., et al. 2003. Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum. Mutat. 21, 28-44. (Pubitemid 36070454)
7. Durbin, R., Eddy, S., Krogh, A., et al. 2003. Biological sequence analysis South Asia edition: probabilistic models of proteins and nucleic acids.
8. Felenstein, J. 2003. Inferring phylogenies. Sinauer Associates, Sunderland, MA.
9. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376. (Pubitemid 11016207)
10. Hein, J., Jensen, J., and Pedersen, C. 2003. Recursions for statistical multiple alignment. Proc. Nat. Acad. Sci. USA 100, 14960.
11. Hein, J., Wiuf, C., Knudsen, B., et al. 2000. Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Mol. Biol. 302, 265-280.
12. Holmes, I. 2004. A probabilistic model for the evolution of RNA structure. BMC Bioinform. 5, 166.
13. Holmes, I., and Bruno, W. 2001. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 17, 803.
14. Joshi, A., Levy, L., and Takahashi, M. 1975. Tree adjunct grammars. J. Comput. Syst. Sci. 10, 136-163.
15. Joshi, A., and Schabes, Y. 1997. Tree-adjoining grammars. Handbook Formal Lang. Beyond Words 3, 69-123.
16. Jukes, T., and Cantor, C. 1969. Evolution of protein molecules. Mammal. Protein Metab. 3, 21-132.
17. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120. (Pubitemid 11166431)
18. Levinson, G., and Gutman, G. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4, 203.
19. Lunter, G. 2007. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. Bioinformatics 23, i289.
20. Lunter, G., Drummond, A., Miklós, I., et al. 2005. Statistical alignment: recent progress, new applications, and challenges. Stat. Methods Mol. Evol. 375-405.
21. Matsui, H., Sato, K., and Sakakibara, Y. 2005. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics 21, 2611-2617. (Pubitemid 40852305)
22. Messer, P., and Arndt, P. 2007. The majority of recent short DNA insertions in the human genome are tandem duplications. Mol. Biol. Evol. 24, 1190.
23. Miklós, I., Lunter, G., and Holmes, I. 2004. A "long indel" model for evolutionary sequence alignment. Mol. Biol. Evol 21, 529.
24. Miklos, I., Novak, A., Satija, R., et al. 2009. Stochastic models of sequence evolution including insertion-deletion events. Stat. Methods Med. Res. 18, 453-448.
25. Rhead, B., Karolchik, D., Kuhn, R., et al. 2009. The UCSC genome browser database: update 2010. Nucleic Acids Res.
26. Rivas, E., and Eddy, S. 2001. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinform. 2, 8.
27. Sammeth, M., and Stoye, J. 2006. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Trans. Comput. Biol. Bioinform. 395-407. (Pubitemid 44950088)
28. Schabes, Y. 1992. Stochastic lexicalized tree-adjoining grammars. Proc. 14th Conf. Comput. Ling. 425-432.
29. Schwartz, S., Kent, W., Smit, A., et al. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13, 103.
30. Siepel, A., and Haussler, D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21, 468.
31. Sinha, S., and Siggia, E. 2005. Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila. Mol. Biol. Evol. 22, 874.
32. Tanay, A., and Siggia, E. 2008. Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 9, R37.
33. The Chimpanzee Genome Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69.
34. Thorne, J., Kishino, H., and Felsenstein, J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34, 3-16.
35. * 1. Theor. Compu. Sci. 210, 277-303. (Pubitemid 129611355)
36. Vijay-Shankar, K., and Joshi, A. 1986. Some computational properties of tree adjoining grammars. Proc. Workshop Strategic Comput. Natural Lang. 223.