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Nucleic Acids Research Advance Access published online on May 7, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn238
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© 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.

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The Jpred 3 secondary structure prediction server

Christian Cole, Jonathan D. Barber and Geoffrey J. Barton*

School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK

*To whom correspondence should be addressed. Tel: +44 1382 385860; Fax: +44 1382 385764; Email: geoff{at}compbio.dundee.ac.uk

Received January 31, 2008. Revised April 2, 2008. Accepted April 15, 2008.

Jpred (http://www.compbio.dundee.ac.uk/jpred) is a secondary structure prediction server powered by the Jnet algorithm. Jpred performs over 1000 predictions per week for users in more than 50 countries. The recently updated Jnet algorithm provides a three-state ({alpha}-helix, β-strand and coil) prediction of secondary structure at an accuracy of 81.5%. Given either a single protein sequence or a multiple sequence alignment, Jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility are made. The predictions are presented as coloured HTML, plain text, PostScript, PDF and via the Jalview alignment editor to allow flexibility in viewing and applying the data. The new Jpred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests. Functional improvements include batch submission of sequences, summary results via email and updates to the search databases. A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions.


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