Skip Navigation


Nucleic Acids Research Advance Access originally published online on June 3, 2008
Nucleic Acids Research 2008 36(Web Server issue):W65-W69; doi:10.1093/nar/gkn283
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4904K) Freely available
Right arrow Screen PDF (597K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_2/W65    most recent
gkn283v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Barquist, L.
Right arrow Articles by Holmes, I.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Barquist, L.
Right arrow Articles by Holmes, I.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W65-W69
© 2008 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.

Articles

xREI: a phylo-grammar visualization webserver

Lars Barquist* and Ian Holmes

Department of Bioengineering, University of California, Berkeley

*To whom correspondence should be addressed. Email: lbarquist{at}gmail.com

Received February 9, 2008. Revised April 16, 2008. Accepted April 26, 2008.

Phylo-grammars, probabilistic models combining Markov chain substitution models with stochastic grammars, are powerful models for annotating structured features in multiple sequence alignments and analyzing the evolution of those features. In the past, these methods have been cumbersome to implement and modify. xrate provides means for the rapid development of phylo-grammars (using a simple file format) and automated parameterization of those grammars from training data (via the Expectation Maximization algorithm). xREI (pron. ‘X-ray’) is an intuitive, flexible AJAX (Asynchronous Javascript And XML) web interface to xrate providing grammar visualization tools as well as access to xrate's training and annotation functionality. It is hoped that this application will serve as a valuable tool to those developing phylo-grammars, and as a means for the exploration and dissemination of such models. xREI is available at http://harmony.biowiki.org/xrei/


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.