Implementation of the Vectorized Position-Specic Iterated Smith-Waterman Algorithm with Heuristic Filtering Algorithm on Cray Architecture

Smith-Waterman is the algorithm for nding local optimal alignments of two amino acid sequences, but is too slow for use in regular large database scanning. We have implemented SW algorithm on Cray X1 architecture, exploiting vectorization and parallelization. In addition we have proposed heuristic database ltering algorithm, which is particularly well suited for the Cray architecture, exploiting possibilities given by the BMM unit.

[1]  J. Wootton,et al.  Analysis of compositionally biased regions in sequence databases. , 1996, Methods in enzymology.

[2]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[3]  S. Karlin,et al.  Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[4]  S. Henikoff,et al.  Amino acid substitution matrices. , 2000, Advances in protein chemistry.

[5]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  John C. Wootton,et al.  Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases , 1993, Comput. Chem..

[8]  Amir Dembo,et al.  LIMIT DISTRIBUTIONS OF MAXIMAL SEGMENTAL SCORE AMONG MARKOV-DEPENDENT PARTIAL SUMS , 1992 .

[9]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.