X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=e42a4e6943e4d64f4c472fbb029800381f4cbef8;hb=57db03ae9b6b80c19901d604b376b41f6fbab31a;hp=669110a213e64a35079471105a185480582df772;hpb=0410fb5d6f4c4e346daf4bb9ad0a78f2e04b4c93;p=jalview.git
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 669110a..e42a4e6 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,85 +1,138 @@
-
-
-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 prediction methods and decides on the
-most likely prediction via a jury network.
-
-- 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→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
-that was first clicked on).
-
-
-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.
-
-
-
-
+
+
+
+JPred Secondary Structure Prediction
+
+
+ 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.
+
+
+