- If nothing is selected, and the displayed sequences appear - to be aligned, then a JNet prediction will be run for the first + 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 JNet prediction + 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 Jnet prediction on + 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: JNet secondary structure prediction is a + 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 - JNet's own reliability score (see below). + JPred's own reliability score (see below).
-The result of a JNet prediction for a sequence is a new +
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 @@ -97,9 +96,14 @@
Coiled-coil predictions for the sequence. These are binary predictions for each location.
Solvent - accessibility predictions - binary predictions of 25%, 5% or 0% - solvent accessibility.
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) +
The consensus prediction - helices are marked as red tubes, and sheets as dark green arrows.
HMM profile based prediction - helices are marked as red tubes, and sheets as dark green arrows.
Jpred prediction - helices are - marked as red tubes, and sheets as dark green arrows.
PSSM based prediction - helices are marked as red tubes, and sheets as dark green arrows.
Amino Acid frequency based - prediction - helices are marked as red tubes, and sheets as dark - green arrows.
A '*' in this annotation indicates that the JNETJURY was invoked to rationalise significantly different primary predictions.