Data Mining in Genomics and ProteomicsView this Special Issue
Research article | Open Access
Anna Gambin, Rafał Otto, "Contextual Multiple Sequence Alignment", BioMed Research International, vol. 2005, Article ID 945084, 8 pages, 2005. https://doi.org/10.1155/JBB.2005.124
Contextual Multiple Sequence Alignment
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.
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.