Parallel syntenic alignments

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

Volumn 2552, Issue , 2002, Pages 420-430

  Futamura, Natsuhiko ^a   Aluru, Srinivas ^a   Huang, Xiaoqiu ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ALIGNMENT; CHROMOSOMES; DNA SEQUENCES; GENES; PARALLEL ALGORITHMS; PARALLEL PROCESSING SYSTEMS;

ALIGNMENT PROBLEMS; DEGREE OF SIMILARITY; GENOMIC DNA; GENOMIC SEQUENCE; HUMAN CHROMOSOMES; SEQUENTIAL ALGORITHM; SYNTENIC REGIONS; TIME-OPTIMAL;

CLUSTERING ALGORITHMS;

EID: 84859718061     PISSN: 03029743     EISSN: 16113349     Source Type: Journal    
DOI: 10.1007/3-540-36265-7_40     Document Type: Article

References (18)

1. S. Aluru, N. Futamura and K. Mehrotra, Biological sequence comparison using prefix computations, Proc. International Parallel Processing Symposium (1999) 653-659. 420
2. M.A. Ansari-Lari, J.C. Oeltjen, S. Schwartz, Z. Zhang, D.M. Muzny, J. Lu, J.H. Gorrell, A. C. Chinault, J.W. Belmont, W. Miller and R.A. Gibbs, Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 andit ssyntenic region in mouse chromosome 6, Genome Research, 8 (1998) 29-40. 429
3. S. Batzoglou, L. Pachter, J. P. Mesirov, B. Berger and E. S. Lander, Human and mouse gene structure: comparative analysis andap plication to exon prediction, Genome Research, 10 (2000) 950-958. 421
4. A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. While and S. L. Salzberg, Alignment of whole genomes. Nucleic Acids Research, 27 (1999) 2369-2376. 421
5. E.W. Edmiston and R.A. Wagner, Parallelization of the dynamic programming algorithm for comparison of sequences, Proc. International Conference on Parallel Processing (1987) 78-80. 420
6. E.W. Edmiston, N.G. Core, J. H. Saltz and R.M. Smith, Parallel processing of biological sequence comparison algorithms, International Journal of Parallel Programming, 17(3) (1988) 259-275. 420
7. O. Gotoh, An improvedalgorit hm for matching biological sequences. Journal of Molecular Biology, 162 (1982) 705-708. 420
8. D. S. Hirschberg, A linear space algorithm for computing maximal common subsequences, Communications of the ACM, 18(6) (1975) 341-343. 423
9. X. Huang, A space-efficient parallel sequence comparison algorithm for a messagepassing multiprocessor, International Journal of Parallel Programming, 18(3) (1989) 223-239. 420
10. X. Huang, A space-efficient algorithm for local similarities, Computer Applications in the Biosciences,6(4) (1990) 373-381. 420
11. X. Huang and K. Chao, A generalized global alignement algorithm, manuscript in preparation. 421
12. N. Jareborg, E. Birney, and R. Durbin, Comparative analysis of noncoding regions of 77 orthologous mouse andh uman gene pairs, Genome Research, 9, (1999) 815-824. 421
13. E. Lander, J.P. Mesirov and W. Taylor, Protein sequence comparison on a data parallel computer, Proc. International Conference on Parallel Processing (1988) 257-263. 420
14. E.W. Mayers and W. Miller, Optimal alignments in linear space, Computer Applications in the Biosciences, 4(1) (1988) 11-17. 420
15. S.B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acidseq uence of two proteins, Journal of Molecular Biology, 48 (1970) 443-453. 420
16. S. Schwartz, Z. Zhang, K. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller, Pip Maker-A web server for aligning two genomic DNA sequences, Genome Research, 10 (2000) 577-586. 421
17. A. Smit and P. Green, http://ftp.genome.washington.edu/RM/RepeatMasker.html, 1999. 429
18. T. F. Smith and M. S. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, 147 (1981) 195-197. 420