Alignments without low-scoring regions

Journal of Computational Biology

Volumn 5, Issue 2, 1998, Pages 197-210

  Zhang, Zheng ^a   Berman, Piotr ^a   Miller, Webb ^a  

^a Pennsylvania State University   (United States)

Author keywords

Dynamic programming; Sequence alignment; Smith Waterman algorithm

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; DATA BASE; GENE SEQUENCE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL;

EID: 0031927028     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1998.5.197     Document Type: Article

References (13)

1. Altschul, S. 1997. Generalized affine gap costs for protein sequence alignment. To appear in Proteins.
2. Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. A basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Altschul, S., Madden, T., Schäffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. 1997. Gapped BLAST and PSI-BLAST - a new generation of protein database search programs. Nucleic Acids Research 25, 3389-3402.
4. Chao, K.-M., Pearson, W., and Miller, W. 1992. Aligning two sequences within a specified diagonal band. CABIOS 8, 481-487.
5. Chao, K.-M., Hardison, R.C., and Miller, W. 1993. Constrained sequence alignment. Bull. Math. Biol. 55, 503-524.
6. Chao, K.-M., Hardison, R.C., and Miller, W. 1994. Recent developments in linear-space alignment methods: a survey. J. Comput. Biol. 1, 271-291.
7. Chao, K.-M., Zhang, J., Ostell, J., and Miller, W. 1997. A tool for aligning very similar DNA sequences. CABIOS 13, 75-80.
8. Gotoh, O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705-708.
9. Johnson, D. 1982. A priority queue in which initialization and queue operations take O(log log D) time. Math. Systems Theory 15, 295-309.
10. Needleman, S.B., and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453.
11. Myers, E., and Miller, W. 1989. Approximate matching of regular expressions. Bull. Math. Biol. 51, 5-37.
12. Spouge, J.L. 1991. Fast optimal alignment. CABIOS 7, 1-7.
13. Zhang, Z., Pearson, W., and Miller, W. 1997. Aligning a DNA sequence with a protein sequence. J. Comput. Biol. 4, 339-349.