Parallelization of multiple genome alignment

Authors:
Yiming Li;Cheng-Kai Chen
Affiliations:
Department of Communication Engineering;Microelectronics and Information Systems Research Center
Venue:
HPCC'05 Proceedings of the First international conference on High Performance Computing and Communications
Year:
2005

Citing 2
Cited 0

Parallel Multiple Sequence Alignment with Dynamic Scheduling

ITCC '05 Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume I - Volume 01
Toward efficient multiple molecular sequence alignment: a system of genetic algorithm and dynamic programming

IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics

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Abstract

In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.