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Bioinformatics Vol. 19 no. 14 2003
Pages 1739-1740
© 2003 Oxford University Press

Applications Note

Designing hardware for protein sequence analysis

Alessandro Marongiu 1, Paolo Palazzari 2,* and Vittorio Rosato 2

1 IPITEC s.r.l.—Rome, Italy and 2 ENEA, Ente per le Nuove Tecnologie, l’Energia e l’Ambiente, Computing and Modeling Unit, Rome, Italy

Received on November 4, 2002 ; revised on February 13, 2003 ; accepted on March 28, 2003

We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.

Availability: the PROSIDIS configuration file and the c code are available at http://www.enea.it/hpcn/php/rosato/

Contact: palazzari{at}casaccia.enea.it

* To whom correspondence should be addressed.


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