A Simple and Space-Efficient Fragment-Chaining Algorithm for Alignment of DNA and Protein Sequences

Applied Mathematics Letters

Volumn 15, Issue 1, 2002, Pages 11-16

  Morgenstern, B ^a,b,c  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b Aventis Pharmaceuticals   (United Kingdom)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Complexity; Dynamic programming; Fragment chaining; Sequence alignment; String algorithm

Indexed keywords

EID: 31244432403     PISSN: 08939659     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0893-9659(01)00085-4     Document Type: Article

References (14)

1. S.B. Needleman and C.D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol. 48, 443-453, (1970).
2. B. Morgenstern, A.W.M. Dress and T. Werner, Multiple DNA and protein sequence alignment based on segment-to-segment comparison, Proc. Natl. Acad. Sci. USA 93, 12098-12103, (1996).
3. B. Morgenstern, DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment, Bioinformatics 15, 211-218, (1999).
4. S. Abdeddaïm and B. Morgenstern, Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB), In Proceedings of the Journées Ouvertes: Biologie, Informatique et Mathématiques (JOBIM), Lecture Notes in Computer Science, (in press).
5. H.-P. Lenhof, B. Morgenstern and K. Reinert, An exact solution for the segment-to-segment multiple sequence alignment problem, Bioinformatics 15, 203-210, (1999).
6. J.D. Kececioglu, H.-P. Lenhof, K. Mehlhorn, P. Mutzel, K. Reinert and M. Vingron, A polyhedral approach to sequence alignment problems, Discrete Applied Mathematics 104, 143-186, (2000).
7. J.W. Wilbur and D.J. Lipman, Rapid similarity searches of nucleic acid and protein data banks, Proc. Natl. Acad. Sci. USA 80, 726-730, (1983).
8. K.-M. Chao and W. Miller, Linear-space algorithms that build local alignments from fragments, Algorithmica 13, 106-134, (1995).
9. D. Eppstein, Z. Galil, R. Giancarlo and G. Italiano, Sparse dynamic programming I: Linear cost functions, J. Assoc. Comput. Mach. 39, 519-545, (1992).
10. D.S. Hirschberg, A linear space algorithm for computing maximal common subsequences, Commun. ACM 18, 314-343, (1975).
11. E.M. Myers and W. Miller, Optimal alignments in linear space, CABIOS 4, 11-17, (1988).
12. B. Morgenstern, A space-efficient algorithm for aligning large genomic sequences, Bioinformatics 16, 948-949.
13. B. Morgenstern, J. Stoye and A.W.M. Dress, Consistent equivalence relations: A set-theoretical framework for multiple sequence alignment, Materialien und Preprints 133, University of Bielefeld, (1999).
14. J.D. Thompson, F. Plewniak, and O. Poch, BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs, Bioinformatics 15, 87-88, (1999).