抄録
We have developed a multiple sequence alignment system which aligns RNA sequences while estimating their stem regions. The system consists of two parts: initialand stem aligners. The initial aligner roughly aligns given RNA sequences using a parallel iterative algorithm based on dynamic programming. The stem aligner refines the rough alignment using a parallel simulated annealing algorithm taking into account connected base pairs in stem regions. In testing with t RNA sequences, the system could generate alignments which identified well-known stem sets of clover shape. We have also developed a stem specifier which monitors such stemregions using a circular representation.
