March 26, 2007 to March 30, 2007
Tim Oliver , Progeniq Pte Ltd., 8 Prince George's Park, Singapore 118407. firstname.lastname@example.org
Leow Yuan Yeow , Progeniq Pte Ltd., 8 Prince George's Park, Singapore 118407. email@example.com
Bertil Schmidt , UNSW Asia, 1 Kay Siang Road, Singapore 248922. Bertil.Schmidt@unswasia.edu.sg
Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared to a database of profile HMMs to detect functional similarities. HMMer is a commonly used package for profile HMM-based methods. However, searching large databases with HMMer suffers from long runtimes on traditional computer architectures. These runtime requirements are likely to become even more severe due to the rapid growth in size of both sequence and model databases. In this paper, we present a new reconfigurable architecture to accelerate HMMer database searching. It is described how this leads to significant runtime savings on off-the-shelf field-programmable gate arrays (FPGAs).
Tim Oliver, Leow Yuan Yeow, Bertil Schmidt, "High Performance Database Searching with HMMer on FPGAs", IPDPS, 2007, 2007 IEEE International Parallel and Distributed Processing Symposium, 2007 IEEE International Parallel and Distributed Processing Symposium 2007, pp. 258, doi:10.1109/IPDPS.2007.370448