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Bioinformatics Advance Access first published online on August 27, 2007
This version published online on August 30, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm398
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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.

TMpro webserver and webservice: Transmembrane helix prediction through amino acid property analysis

Madhavi Ganapathiraju 1,*, Christopher Jon Jursa 2, Hassan A. Karimi 2 and Judith Klein-Seetharaman 1,3,*

1Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA, 2School of Information Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA, 3Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA

*To whom correspondence should be addressed. Prof. Judith Klein-Seetharaman, E-mail: judithks{at}cs.cmu.edu


  Abstract

Summary: TMpro is a transmembrane (TM) helix prediction algorithm that uses language processing methodology for TM segment identification. It is primarily based on the analysis of statistical distributions of properties of amino acids in transmembrane segments. This paper describes the availability of TMpro on the internet via a web interface. The key features of the interface are: (i) Output is generated in multiple formats including a user-interactive graphical chart which allows comparison of TMpro predicted segment locations with other labeled segments input by the user, such as predictions from other methods. (ii) Up to 5000 sequences can be submitted at a time for prediction. (iii) TMpro is published as a web server and a web service so that the method can be accessed by users as well as other services depending on the need for data integration.

Contact: madhavi{at}cs.cmu.edu and judithks{at}cs.cmu.edu

Availability: http://linzer.blm.cs.cmu.edu/tmpro/ (web server and help), http://blm.sis.pitt.edu:8080/axis/services/ TMProFetcherService (web service).

Associate Editor: Prof. Keith Crandall

Received on June 6, 2007; revised on July 24, 2007; accepted on August 2, 2007

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