Markovian structures in biological sequence alignments.

Journal of the American Statistical Association, March, 1999 by Lawrence, Charles E.; Liu, Jun S.; Neuwald, Andrew F.

A novel class of algorithms for the alignment of multiple homologous biopolymer sequences is presented. The proposed method combines the hidden Markov model and the block-based motif model and is therefore sensitive and flexible. The new approach also decomposes the standard hidden Markov model into two components, namely, the insertion component and the deletion component, to provide a rational compromise between biological specificity and model flexibility. The advantages of the method are confirmed by its application to a GTPase family of protein sequences, which yields an alignment that is comparable with known tertiary structures.

1. INTRODUCTION

All of the hereditary information of an individual organism is contained in its genome, which comprises sequences...

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