Abstract

HMMer is a widely used tool for protein sequence homology detection, as well as functional annotation of homologous protein sequences, and protein family classification. The HMMer program is based upon a Viterbi algorithm coded in C, and is quite time consuming. Significant efforts have been undertaken to accelerate this program using custom special purpose hardware, as well as more recent attempts to leverage commodity special purpose hardware. This work will report on several minimally invasive code refactoring efforts independently undertaken by the authors, and their significant performance impact on wall clock execution time of the entire program for various test cases.

Date

April 18, 2006

Authors

Joseph Landman, Joydeep Ray, John Paul Walters

Conference

20th International Conference on Advanced Information Networking and Applications-Volume 1 (AINA'06)

Volume

2

Pages

5 pp.

Publisher

IEEE