X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=396a3a7c0d436523688127aedcc8ce12ee60295f;hb=e23c8a1df90ccbb262f477a1b6c4b49808da80ff;hp=5c3e237a87d526196df499dbdd4ef03e298d066d;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 5c3e237..077ace6 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,7 +1,7 @@
-JNet Secondary Structure Prediction
+JPred Secondary Structure Prediction
- JNet 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
@@ -38,8 +38,7 @@
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
+ href="http://dx.doi.org/10.1093/nar/gkv332">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
@@ -53,35 +52,35 @@
The function available from the
Web Service→Secondary Structure
- Prediction→JNet Secondary Structure Prediction menu does two
+ 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 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
@@ -125,12 +124,12 @@
significantly different primary predictions.
- JNet annotation created in Jalview 2.8.2 and later versions
+ 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.
+ href="../features/annotation.html#seqannots">Add reference
+ annotation Sequence ID popup menu option.
- As of Jalview 2.6, the Jnet service accessed accessed via the
+ 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.