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.

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:

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:

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.