X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=e42a4e6943e4d64f4c472fbb029800381f4cbef8;hb=8fb1345b723e9104cab28c80b352a882e502b1ed;hp=6bd3f1148bf8de99ef14626af8e96d263a450c79;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 6bd3f11..e42a4e6 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
@@ -97,9 +96,14 @@
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.
+ 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.
@@ -113,25 +117,20 @@
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
+ 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
- 'Secondary structure prediction' submenu should be considered a
+ 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.