PROSIDIS: a special purpose processor for protein similarity discovery

This work presents the architecture of PROSIDIS, a special purpose processor designed to search for the occurrence of substrings similar to a given 'template string' within a proteome. The paper recalls the basis of the PHG tool, developed within the framework of the HADES project, which automatically designs a parallel hardware starting from recurrence equations. In this work we present a special purpose processor, designed by PHG, which faces the protein similarity discovery problem. Some results are given, reporting the time spent by several microprocessors and by the PROSIDIS processor to solve the same protein analysis problem.