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.

Keywords

Benchmark (surveying)Probabilistic logicAlignment-free sequence analysisMultiple sequence alignmentConsistency (knowledge bases)Sequence alignmentSequence (biology)Computer scienceData miningRange (aeronautics)BiologyStructural alignmentResource (disambiguation)Computational biologyMachine learningArtificial intelligenceGeneGeneticsPeptide sequence

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Publication Info

Year
2005
Type
article
Volume
15
Issue
2
Pages
330-340
Citations
1129
Access
Closed

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Cite This

Joshua Shulman, Mahathi S.P. Mahabhashyam, Michael Brudno et al. (2005). ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research , 15 (2) , 330-340. https://doi.org/10.1101/gr.2821705

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DOI
10.1101/gr.2821705