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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 alsodoi:10.1093/bioinformatics/bti374 pmid:15797916 fatcat:ijkb6h22zrc6tlu4fir3oplpp4