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+
+JNet Secondary Structure Prediction
+
+
+JNet 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 JNet method uses several different neural networks and decides on
+the most likely prediction via a jury network.
+
+ - 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→JNet 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 JNet 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 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 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
+'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).
+The result of a JNet 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.
+ - JNETSOL25,JNETSOL5,JNETSOL0
+ Solvent accessibility predictions - binary predictions of 25%,
+ 5% or 0% solvent accessibility.
+ - 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.
+ - jpred
+ Jpred 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.
+ - JNETFREQ
+ Amino Acid frequency 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.
+
+
+As of Jalview 2.6, the Jnet 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
+JABAWS Jnet service.
+
+
+