X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=0dfbd1086fcb29152cd57aafe184e4dcee450ff1;hb=8f920d337154e092f5f9056ffde3cdf2735eca43;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index e18e273..0dfbd10 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,18 +1,139 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+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 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→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.
+
+
+ JNet 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 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 JPred4 Rest service.
+
+
+