Optimal alignments in linear space

Bioinformatics

Volumn 4, Issue 1, 1988, Pages 11-17

  Myers, Eugene W ^a,b   Miller, Webb ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY - COMPUTER AIDED ANALYSIS; COMPUTER METATHEORY - ALGORITHMIC LANGUAGES; COMPUTER PROGRAMMING LANGUAGES; COMPUTER SYSTEMS PROGRAMMING - MULTIPROCESSING PROGRAMS;

BIONET; C-SOFTWARE PACKAGE; GOTOH'S ALGORITHM; OPTIMAL SEQUENCE ALIGNMENTS; SPACE LIMITING FACTOR; SPACE-SAVING STRATEGIES;

COMPUTER PROGRAMMING;

ALGORITHM; COMPUTER; COMPUTER ANALYSIS; COMPUTER PROGRAM; GENETIC ENGINEERING;

ALGORITHMS; BASE SEQUENCE; EVOLUTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; SUPPORT, U.S. GOV'T, NON-P.H.S.;

EID: 0023984847     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/4.1.11     Document Type: Article

References (18)

1. Altschul, S. and Erickson, B.W. (1986) Optimal sequence alignments using af-fine gap costs. Bull. Mall. Biol., 48. 606-616.
2. Fickett, J.W. (1984) Fast optimal alignment. Nucleic Adds Res. 12. 175-179.
3. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162. 705-708.
4. Gotoh, O. (1986) Alignment of three biological sequences with an efficient traceback procedure. J. Theor. Biol., 121, 327-337.
5. Gotoh, O. (1987) Pattern matching of biological sequences with limited storage. CABIOS, 3, 17-20.
6. Hirschberg, D.S. (1975) A linear space algorithm for computing longest com¬mon subsequences. Commun. Assoc. Comput. Mach. 18, 341-343.
7. Masek, W.J. and Paterson, M.S. (1980) A faster algorithm for computing string- edit distances. J. Comput. System Sci., 20, 18-31.
8. Miller, W. and Myers, E.W. (1985) A file comparison program. Software- Practice and Experience, 15, 1025-1040.
9. Miller, W. and Myers, E.W. (1988) Sequence comparison with concave weighing functions. Bull. Math. Biol., in press.
10. Myers, E.W. (1986) An (AND) difference algorithm and its variations. Algorithmica, 1, 251-266.
11. Smith, T.F., Waterman, M.S. and Fitch, W.M. (1981) Comparative biosequcnce metrics. J. Mol. Evoi, 18, 38-46.
12. Taylor, P. (1984) A fast homology program for aligning biological sequences. Nucleic Acids Res., 12, 447-455.
13. Ukkonen, E. (1985) Algorithms for approximate string matching. Information and Control, 64, 100-118.
14. Wagner, R.A. and Fischer, M.J. (1974) The string-to-string correction problem. J. ACM, 21, 168-173.
15. Watanabe, K., Urano, Y. and Tamaoki, T. (1985) Optimal alignments of biological sequences on a microcomputer. CABIOS, 1, 83-87.
16. Waterman, M.S. (1983) Sequence alignment in the neighborhood of the optimum. Proc. Natl. Acad. Sci. USA, 80, 3123-3124.
17. Waterman, M.S. and Byers, T.H. (1985) A dynamic programming algorithm to find all solutions in a neighborhood of the optimum. Math. Biosciences, 77, 179-188.
18. Waterman, M.S., Smith, T.F. and Beyer, W.A. (1976) Some biological sequence metrics. Adv. Math., 20, 367-387.