ProbCons swMATH ID: 12014 Software Authors: Chuong B. Do; Mahathi S.P. Mahabhashyam; Michael Brudno; Serafim Batzoglou Description: 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. Homepage: http://genome.cshlp.org/content/15/2/330 Related Software: MUSCLE; ClustalW; MAFFT; T-coffee; DIALIGN; Probalign; Kalign; Balibase; MUMMALS; 3DCoffee; SABmark; Clustal X; DIALIGN-TX; MSAProbs; PCMA; SATe; Mauve; OXBench; M-Coffee; Noisy Cited in: 10 Documents all top 5 Cited by 28 Authors 1 Arribas-Gil, Ana 1 Berkemer, Sarah J. 1 Dabba, Ali 1 Daugelaite, Jurate 1 DeBlasio, Dan 1 Fan, Xiaodan 1 Guo, Xuan 1 Höner zu Siederdissen, Christian 1 Kececioglu, John D. 1 Lárraga-Ramírez, María E. 1 Liu, Jun S. 1 Matias, Catherine 1 Mora-Gutiérrez, Roman Anselmo 1 Morita, Kensuke 1 Nguyen, Ken 1 O’Driscoll, Aisling 1 Pan, Yi 1 Ponsich, Antonin S. 1 Ramírez-Rodríguez, Javier 1 Rincón-García, Eric Alfredo 1 Sakakibara, Yasubumi 1 Sato, Kengo 1 Sleator, Roy D. 1 Stadler, Peter F. 1 Tari, Abdelkamel 1 Warnow, Tandy J. 1 Yuan, Yuan 1 Zouache, Djaafar all top 5 Cited in 8 Serials 1 Journal of Mathematical Biology 1 Computing 1 Statistical Science 1 Statistical Applications in Genetics and Molecular Biology 1 Mathematics in Computer Science 1 Computational Biology 1 ISRN Biomathematics 1 INFOR: Information Systems and Operational Research Cited in 5 Fields 8 Biology and other natural sciences (92-XX) 3 Statistics (62-XX) 2 Operations research, mathematical programming (90-XX) 1 History and biography (01-XX) 1 Computer science (68-XX) Citations by Year