Protein Sequence Alignment by Parallel Iterative Method

Masato Ishikawa
Masaki Hoshida
Makoto Hirosawa
Tomoyuki Toya

Institute for New Generation Computer Technology (ICOT)


We have studied application systems for parallel inference machine developed in ICOT. The systems analyze protein sequences and generate multiple sequence alignments. That analysis is very important in the field of genetic information processing This paper reports two systems: a parallel iterative aligner and a treebased parallel iterative aligner. Although the systems require twice as much execution time as a conventional method, they generate high-quality alignments for even practical-scale problems.