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- Title
HMM-Kalign: a tool for generating sub-optimal HMM alignments.
- Authors
Emmanuelle Becker; Aurélie Cotillard; Vincent Meyer; Hocine Madaoui; Raphaël Guérois
- Abstract
Summary: 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. Availability:http://www-spider.cea.fr/Groups/hk3039/view.html Supplementary information: Supplementary data are available at Bioinformatics online.
- Publication
Bioinformatics, 2007, Vol 23, Issue 22, p3095
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btm492