Bit-parallel computation of local similarity score matrices with unitary weights

International Journal of Foundations of Computer Science

Volumn 17, Issue 6, 2006, Pages 1325-1344

  Hyyrö, Heikki ^a   Navarro, Gonzalo ^b  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b UNIVERSITY OF CHILE   (Chile)

Author keywords

Approximate string matching; Bit parallelism; Local similarity

Indexed keywords

EID: 33845544168     PISSN: 01290541     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0129054106004443     Document Type: Conference Paper

References (14)

1. R. Baeza-Yates and G. Gonnet. A New Approach to Text Searching. Communications of the ACM, 35(10):74-82, 1992.
2. A. Bergeron and S. Hamel. Vector algorithms for approximate string matching. International Journal of Foundations of Computer Science, 13(1):53-65, 2002.
3. M. Crochemore, C. S. Iliopoulos, and Y. J. Pinzon. Speeding-up Hirschberg and Hunt-Szymanski LCS Algorithms. Fundamenta Informaticae, 56(1-2):89-103, 2003.
4. M. Crochemore, G. Landau, and M. Ziv-Ukelson. A sub-quadratic sequence alignment algorithm for unrestricted scoring matrices. In Proc. 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA '02), pages 679-688, 2002.
5. D. Gusfield. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, 1997.
6. H. Hyyrö. Explaining and extending the bit-parallel approximate string matching algorithm of Myers. Technical Report A-2001-10, Dept. of Computer and Information Sciences, University of Tampere, Tampere, Finland, 2001.
7. H. Hyyrö and G. Navarro. Bit-parallel witnesses and their applications to approximate string matching. Algorithmica, 41(3):203-231, 2005.
8. W. Masek and M. Paterson. A faster algorithm for computing string edit distances. J. of Computer and System Sciences, 20:18-31, 1980.
9. G. Myers. A fast bit-vector algorithm for approximate string matching based on dynamic programming. Journal of the ACM, 46(3):395-415, 1999.
10. G. Navarro. A guided tour to approximate string matching. ACM Computing Surveys, 33(1):31-88, 2001.
11. G. Navarro and M. Raffinot. Flexible Pattern Matching in Strings - Practical on-line search algorithms for texts and biological sequences. Cambridge University Press, 2002.
12. S. Smith. Homology Search with Binary and Trinary Scoring Matrices. International Journal of Bioinformatics Research and Applications 2(2):119-131, 2006.
13. H. Tsuji, A. Ishino, and M. Takeda. A Bit-Parallel Tree Matching Algorithm for Patterns with Horizontal VLDC's. In Proc. 12th String Processing and Information Retrieval (SPIRE'05), LNCS 3772, pages 388-398, 2005.
14. S. Wu, U. Manber, and E. Myers. A sub-quadratic algorithm for approximate limited expression matching. Algorithmica, 15(1):50-67, 1996.