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Journal of Biomedicine and Biotechnology
Volume 2005 (2005), Issue 2, Pages 124-131
Research article

Contextual Multiple Sequence Alignment

Institute of Informatics, Warsaw University, Banacha 2, Warsaw 02-097, Poland

Received 30 November 2003; Revised 27 February 2004; Accepted 12 March 2004

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple-alignment setting. To this aim the relaxation of the model was developed (we call this new model averaged contextual alignment) and a new family of amino acids substitution matrices are constructed. In this paper we present a contextual multiple-alignment algorithm and report the outcomes of experiments performed for the BAliBASE test set. The contextual approach turned out to give much better results for the set of sequences containing orphan genes.