title: eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities.
abstract: Probalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. To date, Probalign is among the very best scoring methods on the BAliBASE, HOMSTRAD and OXBENCH benchmarks. Here, we introduce eProbalign, which is an online implementation of the approach. Moreover, the eProbalign web server doubles as an online platform for post-alignment analysis. The heart-and-soul of the post-alignment functionality is the Probalign Alignment Viewer applet, which provides users a convenient means to manipulate the alignments by posterior probabilities. The viewer can also be used to produce graphical and text versions of the output. The eProbalign web server and underlying Probalign source code is freely accessible at http://probalign.njit.edu.
authors.affiliation: Department of Computer Science, New Jersey Institute of Technology, University of North Carolina at Charlotte, USA.
authors.forename: Satish
authors.initials: S
authors.lastname: Chikkagoudar
authors.forename: Usman
authors.initials: U
authors.lastname: Roshan
authors.forename: Dennis
authors.initials: D
authors.lastname: Livesay
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D006801:Humans; D008969:Molecular Sequence Data; D011336:Probability; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D004247:DNA