HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

31/01/2012 - Room C209/10 at 14:00 - External Seminar
Johannes Soeding
(Ludwig-Maximilians-Universität München)
Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments. In this seminar, I will present HHblits (HMM-HMM–based lightning-fast iterative sequence search), an open-source, general-purpose search tool, which represents both query and database sequences by profile-hidden hidden Markov models (HMMs). Compared to the PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50–100% higher sensitivity and generates more accurate alignments. It thus has the potential to improve many downstream analysis and prediction methods. I will first explain how HHblits achieves its sensitivity and speed and then show benchmarks and biological applications. I will finish by demonstrating the use of HHblits on the command line and on the web. Reference: Remmert M., Biegert A., Hauser A., and Soding J. Nat. Methods, in press.
Hosted by: Rodrigo Lopez