title: HMM-Kalign: a tool for generating sub-optimal HMM alignments.
abstract: 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.
authors.affiliation: CEA, iBiTecS, URA 2096, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif sur Yvette, F-91191 France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Becker
authors.forename: Aurélie
authors.initials: A
authors.lastname: Cotillard
authors.forename: Vincent
authors.initials: V
authors.lastname: Meyer
authors.forename: Hocine
authors.initials: H
authors.lastname: Madaoui
authors.forename: Raphaël
authors.initials: R
authors.lastname: Guérois
mesh_terms: D000465:Algorithms; D008390:Markov Chains; D010363:Pattern Recognition, Automated / Q000379:methods; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins