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A rate-based prefiltering approach to blast acceleration

Pnevmatikatos Dionysios, Panagiotis Afratis, Eyripides Sotiriades, Grigorios Chrysos, Sotiria Fytraki

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URIhttp://purl.tuc.gr/dl/dias/8FBDB8F9-26D3-47CA-9695-9E5055618DB4-
Identifierhttps://doi.org/10.1109/FPL.2008.4630026-
Languageen-
Extent4 pagesen
TitleA rate-based prefiltering approach to blast accelerationen
CreatorPnevmatikatos Dionysiosen
CreatorΠνευματικατος Διονυσιοςel
CreatorPanagiotis Afratisen
CreatorEyripides Sotiriadesen
CreatorGrigorios Chrysosen
CreatorSotiria Fytrakien
PublisherInstitute of Electrical and Electronics Engineersen
Content SummaryDNA sequence comparison and database search have evolved in the last years as a field of strong competition between several reconfigurable hardware computing groups. In this paper we present a BLAST preprocessor that efficiently marks the parts of the database that may produce matches. Our prefiltering approach offers significant reduction in the size of the database that needs to be fully processed by BLAST, with a corresponding reduction in the run-time of the algorithm. We have implemented our architecture, evaluated its effectiveness for a variety of databases and queries, and compared its accuracy against the original NCBI Blast implementation. We have found that prefiltering offers at least a factor of 5 and up to 3 orders of magnitude reduction in the database space that needs to be fully searched. Due to its prefiltering nature, our approach can be combined with all major reconfigurable acceleration architectures that have been presented up to date.en
Type of ItemΑφίσα σε Συνέδριοel
Type of ItemConference Posteren
Licensehttp://creativecommons.org/licenses/by/4.0/en
Date of Item2015-10-19-
Date of Publication2008-
Bibliographic CitationP. Afratis, E. Sotiriades, G. Chrysos, S. Fytraki, D. Pnevmatikatos, " A Rate-based prefiltering approach to BLAST acceleration’’, In 2008 Intern. Conf. on Field Progr. Logic and Applications (FPL), pp.631 - 634.doi:10.1109/FPL.2008.4630026en

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