X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=0f64115a86dfa8ba965f432cd551e2ca9df68e3e;hb=a49ce69b89678b3e6ba3c1a61b62d61cc9ee7342;hp=a8727dbee1e32caef2f8538c0d7793fcdc209bb1;hpb=cee65885b13fc0f2d56c1f5df439be1df363e3b1;p=jalview.git
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index a8727db..0f64115 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,15 +1,45 @@
+
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.
-
+
+ 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
@@ -87,5 +117,15 @@ The annotation bars below the alignment are as follows:
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.
+