DocumentCode :
1664162
Title :
PROSIDIS: a special purpose processor for protein similarity discovery
Author :
Marongiu, A. ; Palazzari, P. ; Rosato, V.
Author_Institution :
IPITEC, Rome, Italy
fYear :
2003
Abstract :
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.
Keywords :
biology computing; field programmable gate arrays; parallel algorithms; proteins; search problems; sequences; string matching; systolic arrays; FPGA; HADES project; PHG tool; PROSIDIS; automatic design; biological sequence analysis; microprocessors; parallel hardware; protein analysis problem; protein similarity discovery; proteome; recurrence equations; search; similar substrings; special purpose processor; system of affine recurrence equations; systolic architecture; template string; Biological information theory; Biology computing; Coprocessors; Difference equations; Field programmable gate arrays; Hardware; High level synthesis; Iterative algorithms; Process design; Proteins;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Parallel and Distributed Processing Symposium, 2003. Proceedings. International
ISSN :
1530-2075
Print_ISBN :
0-7695-1926-1
Type :
conf
DOI :
10.1109/IPDPS.2003.1213292
Filename :
1213292
Link To Document :
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