A Statistical Theory of Sequence Alignment with Gaps

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology, ISMB 1998

Volumn , Issue , 1998, Pages 52-58

  Drasdo, Dirk ^a,b   Hwa, Terence ^c   Lässig, Michael ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ALGORITHMS; ALIGNMENT STATISTICS; LOCAL ALIGNMENT; MARKOV SEQUENCE; MUTUAL CORRELATIONS; SCALE INVARIANCE; SCALE-INVARIANT; SEQUENCE ALIGNMENTS; STATISTICAL THEORY; TWO PHASE;

OPTIMAL DETECTION;

DNA; PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; GENETICS; PROBABILITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; STATISTICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DNA; MARKOV CHAINS; MODELS, STATISTICAL; PROTEINS; SEQUENCE ALIGNMENT;

EID: 0031608753     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (25)

1. Altschul, S.F, Gish, W., Muller, W., Myers, E.W., and Lipman, D.J. 1990. Basic Local Alignment Search Tool. J. Mol. Biol. 215, 403-410.
2. Altschul, S.F. and Gish, W. 1996. Local Alignment Statistics. Methods in Enzymology 266, 460-480.
3. Arratia, R. and Waterman, M.S. 1994. A Phase Transition for the Score in Matching Random Sequences Allowing Deletions. Ann. Appi. Prob. 4, 200-225.
4. Gule, D. and Hwa, T. 1998. Static and Dynamic Properties of Inhomogeneous Elastic Media on Disordered Substrate. Phys. Rev. B. in press.
5. Dembo, A. and Karlin, S. 1991. Strong Limit Theorems of Empirical Functionals for Large Exceedances of Partial Sums of IID Variables. Ann. Prob. 19, 1737-1755.
6. Doolittle, R.F. 1996. Methods in Enzymology 266. Academic Press, San Diego.
7. Drasdo, D., Hwa, T. and Lässig, M. 1997. DNA Sequence Alignment and Critical Phenomena. Mat. Res. Soc. Symp. Proc. 263, 75-80.
8. Drasdo D., Hwa, T. and Lässig, M. 1998. Scaling Laws and Similarity Detection in Sequence Alignment with Gaps. Los Alamos e-print archive: physics/9802023.
9. Expósito J.Y., Boute N., Deleage G., Garrone R. 1995. Characterization of two Genes Coding for a Similar Four-Cysteine Motif of the Amino-Terminal Propeptide of a Sea Urchin Fibrillar Collagen. Eur. J. Biochem. 234:59-65.
10. Fehon R.G., Dawson I.A., Artavanis-Tsakonas S. 1994. A Drosophila Homologue of Membrane-Skeleton Protein 4.1 is Associated with Septate Junctions and is Encoded by the Coracle Gene. Development 120:545-557.
11. Halpin-Healy, T. and Zhang, Y.-C. 1995. Kinetic Roughening Phenomena, Stochastic Growth, Directed Polymers and All That: Aspects of Multidisciplinary Statistical Mechanics. Phys. Rep. 254, 215-414.
12. Hwa, T. and Lässig, M. 1996. Similarity Detection and Localization. Phys. Rev. Lett. 76, 2591-2594.
13. Hwa, T. and Lässig, M. 1998. Optimal Detection of Sequence Similarity Ipy Local Alignment. Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB98), in press.
14. 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. U.S.A. 87, 2264-2268.
15. Karlin, S., Dembo, A., and Kawabata, T. 1990. Statistical Composition of High-Scoring Segments from Molecular Sequences. Ann. Stat. 18, 571-581.
16. Krug, J. and Spahn, H. 1991. Kinetic Roughening of Growing Interfaces. In Solids far from equilibrium: Growth, Morphology, and Defects, C. Godreche ed. Cambridge University Press.
17. Licea, C, Newman, CM., and Piza, M.S.T. 1996. Superdiffusitivity in First-Passage Percolation. Prob. Theory Relat. Fields 106 559-591.
18. Licea, C. and Newman. CM. 1996. Geodesies in Two-Dimensional First-Passage Percolation. Ann. Prob. 24 399-410.
19. Muñoz, M.A. and Hwa, T. 1998. On Nonlinear Diffusion with Multiplicative Noise. Europhys. Lett. 41, 147-152.
20. Needleman, S.B. and Wunsch, CD. 1970. A General Method Applicable to tlie Search for Similarities in the Amino Acid Sequences of two Proteins. J. Mol. Biol, 48, 443-453.
21. Smith, T. F. and Waterman, M.S. 1981. Identification of Common Molecular Subsequences. J. Mol. Biol., 147, 195-197.
22. Vingron, M. and Waterman, M.S. 1994. Sequence Alignment and Penalty Choice. Review of Concepts, Case Studies and Implications. J. Mol. Biol 235, 1-12.
23. Waterman, M.S. 1994. Introduction to Computational Biology, Chapman & Hall.
24. Waterman, M.S., and Vingron, M. 1994a. Rapid and Accurate Estimates of Statistical Significance for Sequence Data Base Searches. Proc. Natl. Acad. Sci. U.S.A. 91, 4625-4628.
25. Waterman, M.S. and Vingron, M. 1994b. Sequence Comparison Significance and Poisson Approximation. Stat. Sci. 9, 367-381.