Quasi-consensus-based comparison of profile hidden Markov models for protein sequences

R. Y. Kahsay, G. Wang, G. Gao, L. Liao, R. Dunbrack
2005 Bioinformatics  
A simple approach for the sensitive detection of distant relationships among protein families and for sequence-structure alignment via comparison of hidden Markov models based on their quasi-consensus sequences is presented. Using a previously published benchmark dataset, the approach is demonstrated to give better homology detection and yield alignments with improved accuracy in comparison to an existing state-of-the-art dynamic programming profile-profile comparison method. This method also
more » ... ns significantly faster and is therefore suitable for a server covering the rapidly increasing structure database. A server based on this method is available at
doi:10.1093/bioinformatics/bti374 pmid:15797916 fatcat:ijkb6h22zrc6tlu4fir3oplpp4