Tuesday December 04 2007
CEA
HMM-Kalign: a tool for generating sub-optimal HMM alignments.
Bioinformatics (2007), 23, 3095-3097.
CEA
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.
Becker E, Cotillard A, Meyer V, Madaoui H, Guérois R. (2007). HMM-Kalign: a tool for generating sub-optimal HMM alignments. Bioinformatics. 23(22), 3095-3097.