A tiny step toward Rule-based a Protein Sequence Analysis System

Makoto Hirosawa
Masato Ishikawa
Masaki Hoshida

Institute for New Generation Computer Technology (ICOT)


We will present a paradigm that makes multiple sequence alignment by knowledge.

The technology of multiple alignment of protein is important for protein sequence analysis. So far, many alignment algorithm have been developed. However, they produce just temporary alignment which biologists must refine to produce biologically meaningful alignment.
We interviewed alignment experts and extracted knowledge from them and analyze them. The knowledge was essentially know-how to find possible motifs in the temporary alignment and knowledge on motifs.
Based on this analysis, we formulated alignment system with an aligner and an inteligent refiner which modifies alignment produced by aligner. The intelligent refiner refines the alignment using rules stored in a refinement rule base according to the prioriy of the rules. And Some rules consult biological knowledge base which contains motifs and so on.