Segment-based scores for pairwise eind multiple sequence alignments

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

Volumn , Issue , 1998, Pages 115-121

  Morgenstern, Burkhard ^a   Atchley, William R ^b   Hahn, Klaus ^a   Dress, Andreas ^c  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT PROBLEMS; GLOBAL ALIGNMENT; LOCAL ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; SCORING SCHEMES; SEGMENT-BASED; SEQUENCE ALIGNMENTS; SIMPLE MODIFICATIONS; THRESHOLD PARAMETERS; WEIGHT FUNCTIONS;

PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICS;

AMINO ACID SEQUENCE; ANIMALS; ARTIFICIAL INTELLIGENCE; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0031604259     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. Abdeddaïm, S. 1997, Incremental Computaton of Transitive Closure and Greedy Alignment. Proc. of 8-th Annual Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science 1264, 167 - 179.
2. Altschul, S.F. and Erickson, B.W. 1986. A nonlinear measure of subalignment similarity and its significance levels. Bull. Math. Biol. 48, 617 - 632.
3. Altschul, S.F. and Lipman, D. J. 1989. Trees, Stars and Multiple Biological Sequence Alignment. SIAM J. Appi. Math. 49, 197 - 209.
4. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D. 1990. Basic Local Alignment Search Tool. /. Mol Biol. 215, 403 - 410.
5. Argos, P. and Vingron, M. 1990. Sensitivity Comparison of Protein Amino Acid Sequences. Methods in Enzymology 183, 352 - 365.
6. Atchley, W.R. and Fitch, W.M. 1997. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. 94, 5172 - 5176.
7. Carrillo, H. and Lipman, D. 1988. The multiple sequence alignment problem in biology. SIAM J. Appi. Math. 48, 1073 - 1082.
8. Depiereux, E. and Feytmans, E. 1992. Match-Box: a fundamentally new algorithm for the simultaneous alignment of several protein sequences. CABIOS 8, 501 - 509.
9. Depiereux, E., Baudoux, G., BrifFeuil, P., Reginster, I., De Boll, X., Vinals, C, and Feytmans, E. 1997. Match-Box-erver: a multiple sequence alignment tool placing emphasis on reliability. CABIOS 13, 249 - 256.
10. Feng, D.F., Johnson, M.S., and Doolittle, R. F. 1985. Aligning Amino Acid Sequences: Comparison of Commonly Used Methods. J. Mol. Evol. 21, 112 - 125.
11. Fitch, W.M. and Smith, T. F. 1983. Optimal sequence alignments. Proc. Natl. Acad. Sci. 80, 1382 - 1386.
12. Gotoh, 0. 1986. Alignment of Three Biological Sequences with an Efficient Traceback Procedure. J. Theor. Biol. 121, 327- 337.
13. Henikoff, S. and Henikoff, J. G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89, 10915 - 10919.
14. Karlin, S. and Altschul, S.F. 1993. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. 90, 5873 - 5877.
15. Lawrence, C. E., Altschul, S. F., Boguski, M.S., L i u, J. S., Neuwald, A. F., and Wootton, J. C. 1993. Detecting subtle Sequence Signals: A Gibbs Samphng Strategy for Multiple AUgnment. Science 262, 208 - 213.
16. L i, W.-H. 1997. Molecular Evolution, Sinauer Associates, Inc.
17. McClure, M.A., Vasi, T. K., and Fitch, W.M. 1994. Comparative Analysis of Multiple Protein-Sequence Ahgnment Methods. Mol. Biol. Evol. 11, 571 - 592.
18. Morgenstern, B., Dress, A., and Werner, T. 1996. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. 93, 12098 - 12103.
19. Morgenstern, B. Frech, K., Dress, A., Werner, T. 1998. D I A L I G N: Finding local similarities by multiple sequence alignment. Bioinformatics 14, in press.
20. Murata, M., Richardson, J. S., and Sussman, J. L. 1985. Simultaneous Comparison of three protein sequences. Proc. Natl. Acad. Sci. 82, 3073 - 3077.
21. Needleman, S. and Wunsch, C. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol Biol. 48, 443 - 453.
22. Neuwald, A. F. and Green, P. 1994. Detecting Patterns in Protein Sequences. J. Mol. Biol. 239, 698 - 712.
23. Pearson, W.R. and Lipman, D. J. 1988. Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. 85, 2444 - 2448.
24. Schuler, G.D., Altschul, S.F., and Lipman, D. J. 1991. A Workbench for Multiple Alignment Construction and Analysis. PROTEINS: Structure, Function and Genetics 9, 180 - 190.
25. Smith, T. and Waterman, M. 1981. Comparison of Biosequences. Advances in Applied Mathematics 2, 482 - 489.
26. Smith, R. F. and Smith, T. F. 1992. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secundary structure-dependent gap penalties for use in comparative protein modeling. Protein Eng. 5, 35 - 41.
27. Stoye, J., Moulton, V. and Dress, A. 1997. DCA: An Efficient Implementation of the Divide-and-Conquer Approach to Simultaneous Multiple Sequence Alignment. CABIOS 13, 625 - 626.
28. Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. C L U S T A L W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673 - 4680.
29. Tönges, U., Perrey, S.W., Stoye, J., and Dress, A. 1996. A general method for fast multiple sequence alignment. Gene 172, GC33 - GC41.
30. Vingron, M. and Argos, P. 1991. Motif Recognition and Aligiunent for many Sequences by Comparison of Dot-matrices. J. Mol. Biol. 218, 33 - 43.
31. Vingron, M. and Watermćui, M.S. 1994. Sequence Alignment and Penalty Choice. Review of Concepts, Case Studies and Implications. J. Mot. Biol. 235, 1 - 12.
32. Waterman, M.S. 1986. Multiple sequence alignment by consensus. Nucleic acid research 14, 9095 - 9102.