Acceleration of ungapped extension in Mercury BLAST |
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| Authors: | Joseph Lancaster Jeremy Buhler Roger D Chamberlain |
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| Affiliation: | 1. Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA;2. BECS Technology, Inc., St. Louis, MO, USA;1. Department of Pharmacology & Toxicology, College of Veterinary Medicine, Gyeongsang National University, Jinju Dae-lo 501, Jinju 660-701, Republic of Korea;2. Gyeongnam Livestock Promotion Research Institute, Chojengbuk-lo 104, Jinju 660-985, Gyeongnam, Republic of Korea;3. Department of Animal Science and Biotechnology, Gyeongnam National University of Science and Technology, Jinju 660-758, Republic of Korea;1. Pablo de Olavide University, Carretera de Utrera Km 1 SN, Seville 41013, Spain;2. The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532, USA;1. Department of Mathematics, Bohai University, Jinzhou 121013, PR China;2. Engineering and Technology Research Center of Food Preservation, Processing and Safety Control of Liaoning Province, Jinzhou 121013, PR China;3. Department of Applied Mathematics, Shanghai Institute of Technology, Shanghai 201418, PR China;1. Laboratory of Molecular Genetics, Immunology and Biotechnology, Biology Department, Sciences Faculty of Tunisia, Campus University, 2092 El Manar, Tunis, Tunisia;2. Laboratory of Genetics and Vegetal Biotechnology, Biology Department, Sciences and Technics Faculty, University of Sultan Moulay Slimane, Beni-Mellal, Morocco;1. Centre International de Recherche-Développement sur l’Élevage en zones Subhumides (CIRDES), Unité de recherches sur les bases biologiques de la lutte intégrée, 01 BP 454 Bobo-Dioulasso 01, Burkina Faso;2. Institut de Recherche pour le Développement, Unité Mixte de Recherche IRD-CIRAD 177, TA A-17/G, Campus International de Baillarguet, F-34398 Montpellier, France;3. Wellcome Centre for Molecular Parasitology, University of Glasgow, Biomedical Research Centre, 120 University Place, Glasgow G12 8TA, United Kingdom;4. Programme National de Lutte contre la Trypanosomose Humaine Africaine, BP 851 Conakry, Guinea;5. Université Polytechnique de Bobo-Dioulasso, 01 BP 1091 Bobo-Dioulasso 01, Burkina Faso |
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| Abstract: | The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data efficiently is becoming an increasingly difficult task. There are many available software tools that molecular biologists use for comparing genomic data. This paper focuses on accelerating the most widely used such tool, BLAST. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections to specialized hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone.This paper presents the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and runs at 100 MHz on available FPGAs, making it an effective and powerful component for accelerating biosequence comparisons. The performance of this stage is 25× that of the standard software distribution, yielding close to 50× performance improvement on the complete BLAST application. The sensitivity is essentially equivalent to that of the standard distribution. |
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