Suboptimal alignments improve the detection of weak homologs in sequence database searches

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 153-160

  Li, Yuheng ^a   Lauria, Mario ^a   Bundschuh, Ralf ^b  

^a The Ohio State University   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Forward backward algorithm; Hybrid algorithm; PSI BLAST; Sequence alignment; Suboptimal alignment

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; INFORMATION ANALYSIS; MOLECULAR STRUCTURE; ONLINE SEARCHING; PROTEINS;

FORWARD BACKWARD ALGORITHMS; HYBRID ALGORITHMS; SEQUENCE ALIGNMENT; SUBOPTIMAL ALIGNMENT;

PATTERN RECOGNITION;

EID: 33751159609     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.54     Document Type: Conference Paper

References (31)

1. S. F. Altschul and W. Gish. Local alignment statistics. Methods in Enzymology, 266:460-480, 1996.
2. S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389-3402, September 1997.
3. A. Bateman, E. Birney, R. Durbin, S. R. Eddy, K. L. Howe, and E. L. L. Sonnhammer. The pfam contribution to the annual nar database issure. Nucleic Acids Research, 28(1):263-266, January 2000.
4. L. E. Baum. An inequality and associated maximization technique in statistical estimation of probabilistic functions of a markov process. Inequalities, 3(627): 1-8, 1972.
5. S. E. Brenner, C. Chothia, and T. J. Hubbard. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationship. Proc. Nad. Acad. Sci. USA, 95(11):6073-6078, May 1998.
6. R. Bundschuh. An analytic approach to significance assessment in local sequence alignment with gaps. In S. Istrail and et. al., editors, Proceedings of the fourth annual international conference on Computational molecular biology, pages 86-95, New York, New York, 2000. ACM press.
7. R. Bundschuh. Rapid significance estimation in local sequence alignment with gaps. In S. Istrail and et. al., editors, Proceedings of the fifth annual international conference on Computational molecular biology, pages 77-85, New York, New York, 2001. ACM press.
8. R. Bundschuh. Rapid significance estimation in local sequence alignment with gaps. J. Camp. Biol., 9(2):243-260, April 2001.
9. J. M. Chandonia, N. S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. E. Brenner. Astral compendium enhancements. Nucleic. Acids Research, 30(1):260-263, January 2002.
10. J. F. Collins, A. F. W. Coulson, and A. Lyall. The significance of protein sequence similarities. CABIOS, 4(1):67-71, March 1988.
11. A. Dembo, S. Karlin, and O. Zeitouni. Limit distribution of maximal non-aligned two-sequence segmental score. Ann. Probab., 22(4):2022-2039, October 1994.
12. M. Oerstein and M. Levitt. Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. In Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology, pages 59-67, Menlo Park, California, 1996. AAAI press.
13. L. Holm and C. Sander. Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233(1): 123-138, September 1993.
14. S. Karlin and S. F. Altschul. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A., 87(6):2264-2268, March 1990.
15. S. Karlin and A. Dembo. Limit distributions of the maximal segmental score among markov-dependent partial sums. Adv. Appl. Prob., 24(1): 113-140, 1992.
16. K. Karplus, C. Barrett, and R. Hughey. Hidden markov models for detecting remote protein homologies. Bioinformatics, 14(10): 846-856, November 1998.
17. Y. Li, M. Lauria, and R. Bundschuh. Using hybrid alignment for iterative sequence database searches. Concurrency and Computation: Practice and Experience, 9(16):841-853, August 2004.
18. R. Mott. Maximum likelihood estimation of the statistical distribution of smith-waterman local sequence similarity scores. Bull. Math. Biol., 54(1):59-75, January 1992.
19. R. Mott. Accurate formula for p-values of gapped local sequence and profile alignments. J. Mol. Biol., 300(3):649-659, July 2000.
20. R. Olsen, R. Bundschuh, and T. Hwa. Rapid assessment of extremal statistics for gapped local alignment. In T. Lengauer and et. al., editors, Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, pages 211-222, Menlo Park, California, 1999. AAAI press.
21. J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284(4):1201-1210, December 1998.
22. F. Pearl, A. Todd, I. Sillitoe, M. Dibley, O. Redfern, T. Lewis, C. Bennett, R. Marsden, A. Grant, D. Lee, A. Akpor, M. Maibaum, A. Harrison, T. Dallman, G. Reeves, T. Diboun, S. Addou, S. Lise, C. Johnston, A. Sillero, J. Thornton, and C. Orengo. The cath domain structure database and related resources gene3d and dhs provide comprehensive domain family information for genome analysis. Nucleic Acids Research, 33:247-251, January 2005.
23. W. R. Pearson. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the smith-waterman and fasta algorithms. Genomics, 11(3):635-650, November 1991.
24. W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A., 85(8):2444-2448, April 1988.
25. A. A. Schäfter, L. Aravind, T. L. Madden, S. Shavirin, J. L. Spouge, Y. I. Wolf, E. V. Koonin, and S. F. Altschul. Improving the accuracy of psi-blast protein database searches with composition-based statistics and other refinements. Nucleic Acids Research, 29(14):2994-3005, July 2001.
26. D. Siegmund and B. Yakir. Approximate p-values for sequence alignments. Ann. Stat., 28(3):657-680, June 2000.
27. S. F. Smith and M. S. Waterman. Comparison of biosequences. Adv. Appl. Math., 2:482-489, 1981.
28. M. S. Waterman and M. Vingron. Rapid and accurate estimates of statistical significance for sequence database searches. Proc. Natl. Acad. Sci. USA, 91(11):4625-4628, May 1994.
29. M. S. Waterman and M. Vingron. Sequence comparison significance and poisson approximation. Stat. Sci., 9(3):367-381, August 1994.
30. Y. K. Yu, R. Bundscuh, and T. Hwa. Hybrid alignment: High performance with universal statistics. Bioinformatics, 18(6):864-872, June 2002.
31. Y. K. Yu and T. Hwa. Statistical significance of probabilistic sequence alignment and related local hidden markov models. J. Camp. Biol., 8(3):249-282, June 2001.