ProbCons: probabilistic consistency-based multiple sequence alignment. 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 for this software
References in zbMATH (referenced in 7 articles )
Showing results 1 to 7 of 7.
- Arribas-Gil, Ana; Matias, Catherine: A time warping approach to multiple sequence alignment (2017)
- Nguyen, Ken; Guo, Xuan; Pan, Yi: Multiple biological sequence alignment. Scoring functions, algorithms and evaluation (2016)
- Mora-Gutiérrez, Roman Anselmo; Lárraga-Ramírez, María E.; Rincón-García, Eric A.; Ponsich, Antonin; Ramírez-Rodríguez, Javier: Adaptation of the method of musical composition for solving the multiple sequence alignment problem (2015)
- Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
- Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
- Fan, Xiaodan; Yuan, Yuan; Liu, Jun S.: The EM algorithm and the rise of computational biology (2010)
- Sato, Kengo; Morita, Kensuke; Sakakibara, Yasubumi: PSSMTS: Position specific scoring matrices on tree structures (2008)