The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment

Nucleic Acids Research

Volumn 33, Issue 15, 2005, Pages 4987-4994

  Sheetlin, Sergey ^a   Park, Yonil ^a   Spouge, John L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; INTERNET; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE ALIGNMENT; BIOLOGY; EVALUATION; METHODOLOGY; STATISTICAL ANALYSIS;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 24744434732     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki800     Document Type: Article

References (37)

1. 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.
2. Altschul,S.F., Madden,T.L., Schaffer,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. Nucleic Acids Res., 25, 3389-3402.
3. Robinson,A.B. and Robinson,L.R. (1991) Distribution of glutamine and asparagine residues and their near neighbors in peptides and proteins. Proc. Natl Acad. Sci. USA, 88, 8880-8884.
4. Henikoff S. and Henikoff J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
5. Dayhoff,M.O., Schwartz,R.M. and Orcutt,B.C. (1978) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Spring, MD, Vol. 3, pp. 345-352.
6. Arratia,R. and Waterman,M.S. (1994) A phase transition for the score in matching random sequences allowing deletions. Ann Appl Probab., 4, 200-225.
7. Dembo,A., Karlin,S. and Zeitouni,O. (1994) Limit distributions of maximal non-aligned two-sequence segmental score. Ann Probab., 22, 2022-2039.
8. 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.
9. Mott,R. (1999) Local sequence alignments with monotonic gap penalties. Bioinformatics, 15, 455-462.
10. Mott,R. (2000) Accurate formula for P-values of gapped local sequence and profile alignments. J Mol. Biol., 300, 649-659.
11. Storey,J.D. and Siegmund,D. (2001) Approximate p-values for local sequence alignments: Numerical studies. J Comput. Biol., 8, 549-556.
12. Siegmund,D. and Yakir,B. (2000) Approximate p-values for local sequence alignments. Ann Stat., 28, 657-680.
13. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
14. Waterman,M.S. and Vingron,M. (1994) Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl Acad. Sci. USA, 91, 4625-4628.
15. Olsen,R., Bundschuh,R. and Hwa,T. (1999) Rapid assessment of extremal statistics for gapped local alignment. Proc. Int. Conf. Intell Syst Mol Biol., 211-222.
16. Mott,R. (1992) Maximum-Likelihood-Estimation of the Statistical Distribution of Smith-Waterman Local Sequence Similarity Scores. B Math Biol., 54, 59-75.
17. Smith,T.F., Waterman,M.S. and Burks,C. (1985) The statistical distribution of nucleic acid similarities. Nucleic Acids Res., 13, 645-656.
18. Collins,J.F., Coulson,A.F. and Lyall,A. (1988) The significance of protein sequence similarities. Comput. Appl. Biosci., 4, 67-71.
19. Mott,R. and Tribe,R. (1999) Approximate statistics of gapped alignments. J Comput. Biol., 6, 91-112.
20. Altschul,S.F., Bundschuh,R., Olsen,R. and Hwa,T. (2001) The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res., 29, 351-361.
21. Bundschuh,R. (2002) Rapid significance estimation in local sequence alignment with gaps. J Comput. Biol., 9, 243-260.
22. Grossmann,S. and Yakir,B. (2004) Large deviations for global maxima of independent superadditive processes with negative drift and an application to optimal sequence alignments. Bernoulli, 10, 829-845.
23. Park,Y., Sheetlin,S. and Spouge,J.L. (2005) Accelerated convergence and robust asymptotic regression of the Gumbel scale parameter for gapped sequence alignment. Journal of Physics A: MATHEMATICAL AND GENERAL 38, 97-108.
24. 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.
25. Gotoh,O. (1982) An improved algorithm for matching biological sequences. J Mol. Biol., 162, 705-708.
26. Yu,Y.K. and Hwa,T. (2001) Statistical significance of probabilistic sequence alignment and related local hidden Markov models. J Comput. Biol., 8, 249-282.
27. Montgomery,D.C., Peck,E.A. and Vining,G.G. (2001) Introduction to Linear Regression Analysis. John Wiley & Sons, Inc. NY.
28. Andrews,D.F., Bickel,P.J., Hampel,F.R., Huber,P.J. and rogers,W.H., Tukey,K.W. (1972) Robust Estimates of Location: Survey and advances Princenton University Press, Princenton, NJ.
29. Andrews,D.F. (1974) A robust method for multiple linear regression. Technometrics, 16, 523-531.
30. Huber,P.J. (1964) Robust estimation of a location parameter. Ann. Math. Statist., 35, 73-101.
31. Huber,P.J. (1973) Robust regression: Asymptotics, conjectures and Monte Carlo. Ann Stat, 1, 799-821.
32. Dwass,M. (1970) Probability and Statistics. W.A. Benjamin, NY.
33. Spouge,J.L. (2001) Finite-size corrections to Poisson approximations of rare events in renewal processes. J Appl Probab., 38, 554-569.
34. Spouge,J.L. (2005) Finite-Size Corrections to Poisson Approximations in General Renewal-Success Processes. J Math Anal Appl., 301, 401-418.
35. Spouge,J.L. (2004) Path Reversal and Islands in the Gapped Alignment of Random Sequences. J Appl Probab., 41, 975-983.
36. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
37. Aldous,D. (1989) Probability approximations via the Poisson clumping heuristic. 1st edn. Springer-Verlag, NY.