Designing hardware for protein sequence analysis.
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.


BACKGROUND
the PROSIDIS configuration file and the c code are available at http://www.enea.it/hpcn/php/rosato/
D000465:Algorithms; D000595:Amino Acid Sequence; D003201:Computers; D003205:Computing Methodologies; D017124:Conserved Sequence; D004867:Equipment Design; D019544:Equipment Failure Analysis; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D016415:Sequence Alignment / Q000295:instrumentation / Q000379:methods; D020539:Sequence Analysis, Protein / Q000295:instrumentation* / Q000379:methods*
D011506:Proteins; D020543:Proteome