JPred Secondary Structure Prediction

Secondary structure prediction methods attempts to infer the likely secondary structure for a protein based on its amino acid composition and similarity to sequences with known secondary structure. The most recent version of the method, JPred4, employs a series of neural networks trained to predict different secondary structure types from a sequence profile, and when necessary, employs a jury network to identify the most likely secondary structure prediction.

- Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)
  JPred4: a protein secondary structure prediction server
  Nucleic Acids Research, Web Server issue (first published 15th April 2015)
  http://dx.doi.org/10.1093/nar/gkv332
- Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 secondary structure prediction server Nucleic Acids Research 36 W197-W201
- Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction Proteins 40 502-511

The function available from the Web Service→Secondary Structure Prediction→JPred Secondary Structure Prediction menu does two different kinds of prediction, dependent upon the currently selected region:

- If nothing is selected, and the displayed sequences appear to be aligned, then a JPred prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.
- If just one sequence (or a region on one sequence) has been selected, it will be submitted to the automatic JPred prediction server for homolog detection and prediction.
- If a set of sequences are selected, and they appear to be aligned, then the alignment will be used for a JPred prediction on the first sequence selected in the set (that is, the one nearest the top of the alignment window).

Note: JPred secondary structure prediction is a 'non-column-separable' service - predictions are based on the sequence profile of contiguous stretches of amino-acid sequence. A prediction will only be made on the visible parts of a sequence (see hiding columns) as if it were a contiguous polypeptide chain. Prediction accuracy at the hidden column boundaries may therefore be less than indicated by JPred's own reliability score (see below).

The result of a JPred prediction for a sequence is a new annotated alignment window:

The sequence for which the prediction was made is the first one in the alignment. If a sequence based prediction was made then the remaining sequences in the alignment are the aligned parts of homologs which were used to construct a sequence profile for the prediction. If the prediction was made using a multiple alignment, then the original multiple alignment will be returned, annotated with the prediction.

The annotation bars below the alignment are as follows:

- Lupas_21, Lupas_14, Lupas_28
  Coiled-coil predictions for the sequence. These are binary predictions for each location.
- Jnet Burial
  Prediction of Solvent Accessibility. levels are
  - 0 - Exposed
  - 3 - 25% or more S.A. accessible
  - 6 - 5% or more S.A. accessible
  - 9 - Buried (<5% exposed)
- JNetPRED
  The consensus prediction - helices are marked as red tubes, and sheets as dark green arrows.
- JNetCONF
  The confidence estimate for the prediction. High values mean high confidence. prediction - helices are marked as red tubes, and sheets as dark green arrows.
- JNetALIGN
  Alignment based prediction - helices are marked as red tubes, and sheets as dark green arrows.
- JNetHMM
  HMM profile based prediction - helices are marked as red tubes, and sheets as dark green arrows.
- JNETPSSM
  PSSM based prediction - helices are marked as red tubes, and sheets as dark green arrows.
- JNETJURY
  A '*' in this annotation indicates that the JNETJURY was invoked to rationalise significantly different primary predictions.

JPred annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the Add reference annotation Sequence ID popup menu option. As of Jalview 2.6, the JPred service accessed accessed via the 'Secondary structure prediction' submenu should be considered a legacy Jalview SOAP service, and will be replaced in the near future by a JPred4 Rest service.