Proc. of FGCS '94, ICOT, Tokyo, December 1994

Parallel Application Systems in Genetic Information Processing

Masato Ishikawa, Tomoyuki Toya And Yasushi Totoki

Institute For New Generation Computer Technology
4-28-21f, Mita 1-chome, Minato-ku, Tokyo 108, Japan
ishikawa@icot.or.jp

Abstract:

We have developed parallel application systems for genetic sequence analysis. The systems are three parallel iterative aligners and an alignment workbench for the aligners. The parallel iterative aligners use a best-first search, a hill-climbing search, and a genetic algorithm. Each iterative aligner can produce higher-quality solutions than the conventional tree-based aligner. The genetic algorithm shows better performance than the best-first and hill-climbing searches. The alignment workbench, which features the parallel iterative aligners, realizes alignment which is not only fast and high-quality-it is also constraint-based. When a user has some biological knowledge which indicates that some characters might be aligned in a column, a constraint can be defined for those characters. The constraint set is considered simultaneously in each iteration cycle of parallel alignment. Then appropriate multiple alignment is generated by the aligner and displayed on the workbench's full-color display. The alignment workbench also contains the following characteristic sequence analysis modules: a phylogenetic tree drawer, a motif-database matcher, and a stem region specifier.

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