ProbCons: Probabilistic consistency-based multiple sequence alignment.

Chuong B Do; Mahathi S P Mahabhashyam; Michael Brudno; Serafim Batzoglou

doi:10.1101/gr.2821705

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ProbCons: Probabilistic consistency-based multiple sequence alignment.

Chuong B Do·Mahathi S P Mahabhashyam·Michael Brudno·Serafim Batzoglou

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Abstract

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark data sets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource.

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Algorithms Amino Acid Sequence Benchmarking Computational Biology Databases, Protein Genetic Variation Molecular Sequence Data Sequence Alignment Software Software Validation Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Chuong B Do, Mahathi S P Mahabhashyam, Michael Brudno, Serafim Batzoglou. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment.. https://doi.org/10.1101/gr.2821705

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