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Bioinformatics. 2007 Nov 15;23(22):3095-7. Epub 2007 Oct 6.

HMM-Kalign: a tool for generating sub-optimal HMM alignments.

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  • 1CEA, iBiTecS, URA 2096, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif sur Yvette, F-91191 France.


Recent development of strategies using multiple sequence alignments (MSA) or profiles to detect remote homologies between proteins has led to a significant increase in the number of proteins whose structures can be generated by comparative modeling methods. However, prediction of the optimal alignment between these highly divergent homologous proteins remains a difficult issue. We present a tool based on a generalized Viterbi algorithm that generates optimal and sub-optimal alignments between a sequence and a Hidden Markov Model. The tool is implemented as a new function within the HMMER package called hmmkalign.

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