Aligning alignments

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1448 LNCS, Issue , 1998, Pages 189-208

  D Kececioglu, John ^a   Zhang, Weiqing ^b  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Affine gap costs; Profiles 1 Introduction While; Quasi natural gap costs; Sequence comparison; Sum of pMrs alignment

Indexed keywords

BIOLOGICAL SEQUENCES; COMPUTATIONAL BIOLOGY; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; OBJECTIVE FUNCTIONS; PROFILES 1 INTRODUCTION WHILE; QUASI-NATURAL GAP COSTS; SEQUENCE COMPARISONS;

ALGORITHMS; BIOINFORMATICS; PATTERN MATCHING;

COSTS;

EID: 84877316776     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: None     Document Type: Conference Paper

References (25)

1. Altschul, S. F. "Gap costs for multiple sequence alignment. " Journal of Theoretical Biology 138, 297-309, 1989.
2. Anson, E. L. and E. W. Myers. "ReAligner: a program for refining DNA sequence multi-alignments. " Proceedings of the 1st ACM Conference on Computational Molecular Biology, 9-13, 1997.
3. Carrillo, H. and D. Lipman. "The multiple sequence alignment problem in biology. " SIAM Journal on Applied Mathematics 48, 1073-1082, 1988.
4. Dayhoff, M. O., R. M. Schwartz and B. C. Orcutt. "A model of evolutionary change in proteins. " In Atlas of Protein Sequence and Structure 5:3, M. O. Dayhoff editor, 345-352, 1978.
5. Fredman, M. L. "Algorithms for computing evolutionary similarity measures with length independent gap penalties. " Bulletin of Mathematical Biology 46:4, 553-566, 1984.
6. Galil, Z. and R. Giancarlo. "Speeding up dynamic programming with applications to molecular biology. " Theoretical Computer Science 64, 107-118, 1989.
7. Gotoh, O. "An improved algorithm for matching biological sequences. " Journal of Molecular Biology 162, 705-708, 1982.
8. Gotoh, O. "Optimal alignment between groups of sequences and its application to multiple sequence alignment. " Computer Applications in the Biosciences 9:3, 361-370, 1993.
9. Gotoh, O. "Further improvement in methods of group-to-group sequence alignment with generalized profile operations. " Computer Applications in the Biosciences 10:4, 379-387, 1994.
10. Gribskov, M., A. D. McLachlan, and D. Eisenberg. "Profile analysis: detection of distantly related proteins. " Proceedings of the National Academy of Sciences USA 84, 4355-4358, 1987.
11. Gupta, S., J. Kececioglu and A. Schäffer. "Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. " Journal of Computational Biology 2:3, 459-472, 1995.
12. Gusfield, D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York, 1997.
13. Henikoff, S. and J. G. Henikoff. "Amino acid substitution matrices from protein blocks. " Proceedings of the National Academy of Sciences USA 89, 10915-10919, 1992.
14. Hirschberg, D. S. "A linear space algorithm for computing longest common subsequences. " Communications of the A CM 18, 341-343, 1975.
15. Lipman, D. G., S. F. Altschul and J. D. Kececioglu. "A tool for multiple sequence alignment. " Proceedings of the National Academy of Sciences USA 86, 4412-4415, 1989.
16. Miller, W. and E. W. Myers. "Sequence comparison with concave weighting functions. " Bulletin of Mathematical Biology 50, 97-120, 1988.
17. Myers, E. W. and W. Miller. "Optimal alignments in linear space. " Computer Applications in the Biosciences 4:1, 11-17, 1988.
18. Myers, G., S. Selznick, Z. Zhang and W. Miller. "Progressive multiple alignment with constraints. " Proceedings of the 1st ACM Conference on Computational Molecular Biology, 220-225, 1997.
19. Sankoff, D. and J. B. Kruskal, editors. Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA, 1983.
20. Setubal, J. and J. Meidanis. Introduction to Computational Molecular Biology. PWS Publishing Company, Boston, 1997.
21. Taylor, E. W., A. Bhat, R. Nadimpalli, W. Zhang and J. D. Kececioglu. "HIV-1 encodes a sequence overlapping env gp41 with highly significant similarity to selenium dependent glutathione peroxidases. " Journal of Acquired Immune Deficiency Syndromes and Human Retrovirotogy 15:5, 393-394, 1997.
22. Wang, L. and T. Jiang. "On the complexity of multiple sequence alignment. " Journal of Computational Biology 1:4, 337-348, 1994.
23. Waterman, M. S. "Efficient sequence alignment algorithms. " Journal of Theoretical Biology 108, 333-337, 1984.
24. Waterman, M. S. Introduction to Computational Biology: Maps, Sequences, and Genomes. Chapman and Hall, London, 1995.
25. Zhang, W., J. D. Kececioglu and E. W. Taylor. "Assessing distant homology between an aligned protein family and a proposed member through accurate sequence alignment. " Technical Report 97-3, Department of Computer Science, The University of Georgia, October 1997. Submitted to Journal of Molecular Biology.