Accelerating HMMer searches on Opteron processors with minimally invasive recoding
Joseph Landman, Jeffrey Scott Ray, John Paul Walters · 2006
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.