A practical approach to significance assessment in alignment with gaps

Journal of Computational Biology

Volumn 13, Issue 2, 2006, Pages 429-441

  Chia, Nicholas ^a   Bundschuh, Ralf ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Gumbel distribution; Markov models and or hidden markov models; Pairwise sequence alignment; Statistical significance; Statistics of motifs or strings

Indexed keywords

CONFERENCE PAPER; GUMBEL DISTRIBUTION; HIDDEN MARKOV MODEL; MARKOV MODEL; PAIRWISE SEQUENCE ALIGNMENT; PRIORITY JOURNAL; PROTEIN MOTIF; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL DISTRIBUTION; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 33645998128     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.429     Document Type: Conference Paper

References (43)

1. Altschul, S.F., Bundschuh, R., Olsen, R., and Hwa, T. 2001. The estimation of statistical parameters for local alignment score distributions. Nucl. Acids Res. 29, 351-361.
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. Altschul, S.F., and Gish, W. 1996. Local alignment statistics. Methods Enzymol. 266, 460-480.
4. 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.
5. Boutet de Monvel, J. 1999. Extensive simulations for longest common subsequences. Eur. Phys. J. B 7, 293-308.
6. Boutet de Monvel, J. 2000. Mean-field approximations to the longest common subsequence problem. Phys. Rev. E 62, 204-209.
7. Bundschuh, R. 2000. An analytic approach to significance assessment in local sequence alignment with gaps. Proc. 4th Ann. Int. Conf. on Computational Molecular Biology (RECOMB '00), 86-95.
8. Bundschuh, R. 2001. High precision simulations of the longest common subsequence problem. Eur. Phys. J. B 22, 533-541.
9. Bundschuh, R. 2002. Asymmetric exclusion process and extremal statistics of random sequences. Phys. Rev. E 65, 031911.
10. Bundschuh, R., and Hwa, T. 2000. An analytic study of the phase transition line in local sequence alignment with gaps. Disc. Appl. Math. 104, 113-142.
11. Chia, N., and Bundschuh, R. 2004. Finite width model sequence comparison. Phys. Rev. E 70, 021906.
12. Collins, J.F., Coulson, A.F.W., and Lyall, A. 1988. The significance of protein sequence similarities. CABIOS 4, 67-71.
13. Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. 1978. A model of evolutionary change in proteins, Atlas of Protein Sequence and Structure, 5(Suppl. 3), 345-358.
14. Dančík, V. 1994. Expected Length of Longest Common Subsequences. Ph.D thesis, University of Warwick.
15. Dančík, V., and Paterson, M. 1994. Longest common subsequences. Proc. 19th Int. Symp. Mathematical Foundations of Computer Science, Lecture Notes in Computer Science 841, 127-142.
16. Derrida, B., and Appert, C. 1999. Universal large-deviation function of the Karder-Parisi-Zhang equation in one dimension. J. Stat. Phys. 94, 1-30.
17. Derrida, B., and Lebowitz, J.L. 1998. Exact large deviation function in the asymmetric exclusion process. Phys. Rev. Lett. 80, 209-213.
18. Doolittle, R.F., Ed. 1996. Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, Vol. 266, Academic Press, San Diego, CA.
19. Drasdo, D., Hwa, T., and Lassig, M. 2001. Scaling laws and similiarity detection in sequence alignment with gaps. J. Comp. Biol. 1, 115-141.
20. Gumbel, E.J. 1958. Statistics of Extremes, Columbia University Press, New York.
21. Henikoff, S., and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
22. Hwa, T., and Lässig, M. 1996. Similiarity-detection and localization. Phys. Rev. Lett. 76, 2591-2594.
23. Kardar, M., Parisi, G., and Zhang, Y.C. 1986. Dynamic scaling of growing surfaces. Phys. Rev. Lett. 56, 889-892.
24. Karlin, S., and Altschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87, 2264-2268.
25. Karlin, S., and Altschul, S.F. 1993. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA 90, 5873-5877.
26. Karlin, S., and Dembo, A. 1992. Limit distributions of the maximal segmental score among Markov-dependent partial sums. Adv. Appl. Prob. 24, 113-140.
27. Lehoucq, R.B. 1997. Truncated QR algorithms and the numerical solution of large scale eigenvalue problems. Preprint MCS-P648-0297, Argonne National Laboratory, Argonne, IL.
28. Lehoucq, R.B., and Scott, J.A. 1996. An evaluation of software for computing eigenvalues of sparse nonsymmetric matrices. Preprint MCS-P547-1195, Argonne National Laboratory, Argonne, IL.
29. Lehoucq, R.B., Sorensen, D.C., and Yang, C. 1997. ARPACK Users' Guide: Solutions of Large Scale Eigenvalue Problems with Implicitly Restarted Arnoldi Methods, SIAM, Philadelphia, PA.
30. Mott, R. 1992. Maximum likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores. Bull. Math. Biol. 54, 59-75.
31. Mott, R. 1999. Accurate estimate of p-values for gapped local sequence alignment. Private communication.
32. Mott, R., and Tribe, R. 1999. Approximate statistics of gapped alignments. J. Comp. Biol. 6, 91-112.
33. Needleman, S.B., and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
34. Olsen, R., Bundschuh, R., and Hwa, T. 1999. Rapid assessment of extremal statistics for gapped local alignment. Proc. 7th Int. Conf. on Intelligent Systems for Molecular Biology, 211-222.
35. Pearson, W.R. 1991. Searching protein sequence libraries. Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635-650.
36. Siegmund, D., and Yakir, B. 2000. Approximate p-values for sequence alignments. Ann. Statist. 28, 657-680.
37. Smith, S.F., and Waterman, M.S. 1981. Comparison of biosequences. Adv. Appl. Math. 2, 482-489.
38. Smith, T.F., Waterman, M.S., and Burks, C. 1985. The statistical distribution of nucleic acid similarities. Nucl. Acids Res. 13, 645-656.
39. Sorensen, D.C. 1992. Implicit application of polynomial filters in a k-step Arnoldi method. SIAM J. Matrix Analysis and Applications 13, 357-385.
40. Waterman, M.S. 1994. Introduction to Computational Biology, Chapman and Hall, London.
41. Waterman, M.S., Gordon, L., and Arratia, R. 1987. Phase transitions in sequence matches and nucleic acid structure. Proc. Natl. Acad. Sci. USA 84, 1239-1243.
42. Waterman, M.S., and Vingron, M. 1994. Sequence comparison significance and Poisson approximation. Stat. Sci. 9, 367-381;
43. Rapid and accurate estimates of statistical significance for sequence database searches. Proc. Natl. Acad. Sci. USA 91, 4625-4628.