RT Journal
A1 Do, Chuong B.
A1 Mahabhashyam, Mahathi S.P.
A1 Brudno, Michael
A1 Batzoglou, Serafim
T1 ProbCons: Probabilistic consistency-based multiple sequence alignment
JF Genome Research 
JO Genome Research 
YR 2005 
FD February 01 
VO 15 
IS 2 
SP 330 
OP 340 
DO 10.1101/gr.2821705 
UL http://genome.cshlp.org/content/15/2/330.abstract 
AB 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.