PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery

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International Parallel and Distributed Processing Symposium (IPDPS'03)

Nice, France

April 22-April 26

ISBN: 0-7695-1926-1

	ASCII Text	x
	A. Marongiu, P. Palazzari, V. Rosato, "PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery," Parallel and Distributed Processing Symposium, International, pp. 155b, International Parallel and Distributed Processing Symposium (IPDPS'03), 2003.

	BibTex	x
	@article{ 10.1109/IPDPS.2003.1213292, author = {A. Marongiu and P. Palazzari and V. Rosato}, title = {PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery}, journal ={Parallel and Distributed Processing Symposium, International}, volume = {0}, year = {2003}, issn = {1530-2075}, pages = {155b}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2003.1213292}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Parallel and Distributed Processing Symposium, International TI - PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery SN - 1530-2075 SP EP A1 - A. Marongiu, A1 - P. Palazzari, A1 - V. Rosato, PY - 2003 KW - biological sequence analysis KW - FPGA KW - systolic architecture KW - System of Affine Recurrence Equations VL - 0 JA - Parallel and Distributed Processing Symposium, International ER -

A. Marongiu, IPITEC

P. Palazzari, ENEA

V. Rosato, ENEA

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/IPDPS.2003.1213292

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.

Index Terms:

biological sequence analysis, FPGA, systolic architecture, System of Affine Recurrence Equations

Citation:

A. Marongiu, P. Palazzari, V. Rosato, "PROSIDIS: A Special Purpose Processor for PROtein SImilarity DIScovery," ipdps, pp.155b, International Parallel and Distributed Processing Symposium (IPDPS'03), 2003

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