Abstract

HMMER, based on the profile Hidden Markov Model (HMM) is one of the most widely used sequence database searching tools, allowing researchers to compare HMMs to sequence databases or sequences to HMM databases. Such searches often take many hours and consume a great number of CPU cycles on modern computers. We present a cluster-enabled hardware/software-accelerated implementation of the HMMER search tool hmmsearch. Our results show that combining the parallel efficiency of a cluster with one or more high-speed hardware accelerators (FPGAs) can significantly improve performance for even the most time consuming searches, often reducing search times from several hours to minutes.

Date

September 1, 2007

Authors

John Paul Walters, Xiandong Meng, Vipin Chaudhary, Tim Oliver, Leow Yuan Yeow, Bertil Schmidt, Darran Nathan, Joseph Landman

Journal

The Journal of VLSI Signal Processing

Volume

48

Issue

3

Pages

223-238

Publisher

Springer Netherlands