The Jpred 3 secondary structure prediction server

Abstract

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, beta-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.

Figure 1.

Examples of progress of a submission to Jpred. A screenshot of a list of hits to the PDB (background) and of the Jpred progress meter (foreground). The ‘continue’ button on the PDB hits page allows the user to continue on to the submission of a secondary structure prediction job.

Figure 2.

Jpred results viewing options. The ‘Full HTML’, ‘PDF’ and ‘Jalview’ views of the results are shown for the same query sequence and the different representations of the secondary structure, solvent accessibility and coiled-coil predictions can be compared.