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Bioinformatics Advance Access originally published online on May 7, 2009
Bioinformatics 2009 25(14):1761-1767; doi:10.1093/bioinformatics/btp302
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

Anna Lobley 1,{dagger}, Michael I. Sadowski 2,{dagger} and David T. Jones 1,*

1 Department of Computer Science, University College London, London WC1E 6BT and 2 Division of Mathematical Biology, National Institute of Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK

* To whom correspondence should be addressed.


  Abstract

Motivation: Generation of structural models and recognition of homologous relationships for unannotated protein sequences are fundamental problems in bioinformatics. Improving the sensitivity and selectivity of methods designed for these two tasks therefore has downstream benefits for many other bioinformatics applications.

Results: We describe the latest implementation of the GenTHREADER method for structure prediction on a genomic scale. The method combines profile–profile alignments with secondary-structure specific gap-penalties, classic pair- and solvation potentials using a linear combination optimized with a regression SVM model. We find this combination significantly improves both detection of useful templates and accuracy of sequence-structure alignments relative to other competitive approaches. We further present a second implementation of the protocol designed for the task of discriminating superfamilies from one another. This method, pDomTHREADER, is the first to incorporate both sequence and structural data directly in this task and improves sensitivity and selectivity over the standard version of pGenTHREADER and three other standard methods for remote homology detection.

Contact: d.jones{at}cs.ucl.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Thomas Lengauer

Received on November 24, 2008; revised on April 20, 2009; accepted on May 4, 2009

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