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ProbCons: Probabilistic consistency-based multiple sequence alignment
Open accessAbstract
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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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
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Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Phylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533
Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Auxin-related gene families in abiotic stress response in Sorghum bicolor
Wang, S., Bai, Y., Shen, C., Wu, Y., Zhang, S., Jiang, D., Guilfoyle, T. J., Chen, M., & Qi, Y. (2010) · Functional & Integrative Genomics · doi:10.1007/s10142-010-0174-3 · Cited by 297
Metadata
- Authors
- Do, C. B., Mahabhashyam, M. S. P., Brudno, M., & Batzoglou, S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2005-02
- Volume
- 15
- Issue
- 2
- Pages
- 330-340
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2140872496
- Cited by
- 1,114
- References
- 2
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Do, C. B., Mahabhashyam, M. S. P., Brudno, M., & Batzoglou, S. (2005). ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research. https://doi.org/10.1101/gr.2821705
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