Align-m--a new algorithm for multiple alignment of highly divergent sequences.

Ivo Van Walle; Ignace Lasters; Lode Wyns

doi:10.1093/bioinformatics/bth116

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Align-m--a new algorithm for multiple alignment of highly divergent sequences.

Ivo Van Walle·Ignace Lasters·Lode Wyns

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Abstract

MOTIVATION: Multiple alignment of highly divergent sequences is a challenging problem for which available programs tend to show poor performance. Generally, this is due to a scoring function that does not describe biological reality accurately enough or a heuristic that cannot explore solution space efficiently enough. In this respect, we present a new program, Align-m, that uses a non-progressive local approach to guide a global alignment. RESULTS: Two large test sets were used that represent the entire SCOP classification and cover sequence similarities between 0 and 50% identity. Performance was compared with the publicly available algorithms ClustalW, T-Coffee and DiAlign. In general, Align-m has comparable or slightly higher accuracy in terms of correctly aligned residues, especially for distantly related sequences. Importantly, it aligns much fewer residues incorrectly, with average differences of over 15% compared with some of the other algorithms. AVAILABILITY: Align-m and the test sets are available at http://bioinformatics.vub.ac.be

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Algorithms Amino Acid Sequence Genetic Variation Molecular Sequence Data Proteins Reproducibility of Results Sensitivity and Specificity Sequence Alignment Sequence Analysis, Protein Sequence Homology, Amino Acid Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't Validation Study

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Ivo Van Walle, Ignace Lasters, Lode Wyns. 2004-02-12. Align-m--a new algorithm for multiple alignment of highly divergent sequences.. https://doi.org/10.1093/bioinformatics%2Fbth116

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