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IPPS
2003
IEEE

PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery

13 years 9 months ago
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 in 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. Keywords biological sequence analysis, FPGA, systolic architecture, System of Affine Recurrence Equations.
Alessandro Marongiu, Paolo Palazzari, Vittorio Ros
Added 04 Jul 2010
Updated 04 Jul 2010
Type Conference
Year 2003
Where IPPS
Authors Alessandro Marongiu, Paolo Palazzari, Vittorio Rosato
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