Designing hardware for protein sequence analysis

descriptionPublicationkeyboard_double_arrow_right Article 22 Sep 2003 Italy English Publisher:Oxford University Press (OUP)Journal:Bioinformatics, volume 19, pages 1,739-1,740 (issn: 1367-4803, eissn: 1367-4811,

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Authors: Alessandro Marongiu; Paolo Palazzari; Vittorio Rosato;

doi: 10.1093/bioinformatics/btg228

pmid: 14512343

Designing hardware for protein sequence analysis

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Abstract

Abstract 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/

Country

Italy

Related Organizations

National Institute for Nuclear Physics
Italy

Keywords

Statistics and Probability, Proteomics, Proteome, Computers, Molecular Sequence Data, Proteins, Equipment Design, Biochemistry, Computing Methodologies, Computer Science Applications, Equipment Failure Analysis, Computational Mathematics, Computational Theory and Mathematics, Sequence Analysis, Protein, Amino Acid Sequence, Molecular Biology, Sequence Alignment, Algorithms, Conserved Sequence

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