accelerating string set matching in fpga hardware for bioinformatics research加速生物信息学研究在fpga硬件设置匹配字符串.pdfVIP

BMC Bioinformatics BioMed Central Methodology article Open Access Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research Yoginder S Dandass*†1,2, Shane C Burgess1,3,4, Mark Lawrence1,4 and Susan M Bridges†1,2 Address: 1Institute of Digital Biology, Mississippi State University, Mississippi, 39762, USA, 2Department of Computer Science and Engineering, Mississippi State University, Mississippi, 39762, USA, 3Life Science and Biotechnology Institute, College of Veterinary Medicine, Mississippi State University, Mississippi, 39762, USA and 4Department of Basics Science, Mississippi State University, Mississippi, 39762, USA Email: Yoginder S Dandass* - yogi@; Shane C Burgess - burgess@; Mark Lawrence - lawrence@; Susan M Bridges - bridges@ * Corresponding author †Equal contributors Published: 15 April 2008 Received: 4 January 2008 Accepted: 15 April 2008 BMC Bioinformatics 2008, 9:197 doi:10.1186/1471-2105-9-197 This article is available from: /1471-2105/9/197 © 2008 Dandass et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The process of matching peptide sequences against a ge