HMMER for Cell BE |
HMMER is a popular genome analysis package based on Hidden Markov Models. It’s main utility called hmmsearch is used for sensitive profile HMM search for genomic sequences homologues.
During the work on Cell Broadband Engine port of HMMER we developed parallelized version of hmmsearch based on HMMER-Cell project and HMMER-Altivec port. Resulted solution is capable to fully utilize Cell BE computational power - using all features of this specific and really high-performance processor we gained a speedup factor of 10x compared to realization running on modern Core2 Quad and a speedup factor of 100x compared to non-optimized version of HMMER running on Cell BE.
An essential point for regular biologists is that optimized package is accessible from user-friendly and easy-to-use visual interface of UGENE.
Please visit our downloads page to get Cell-compatible version of UGENE.
You can see results of our benchmarks on the figures below:
