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Bioinformatics. 2005 May 15;21(10):2287-93. Epub 2005 Mar 29.

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

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  • 1Delaware Biotechnology Institute, Newark, DE 19715, USA.


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 runs significantly faster and is therefore suitable for a server covering the rapidly increasing structure database. A server based on this method is available at

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