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Nucleic Acids Research Advance Access published online on May 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm267
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities

Satish Chikkagoudar1, Usman Roshan1,* and Dennis Livesay2

1Department of Computer Science, New Jersey Institute of Technology and 2Department of Computer Science and Bioinformatics Research Center, University of North Carolina at Charlotte

*To whom correspondence should be addressed. Tel: +1-973-596-2872; Fax: +1-973-596-5777; Email: usman{at}cs.njit.edu

Received February 2, 2007. Revised March 29, 2007. Accepted April 8, 2007.

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


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