X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=077ace642ce87a66c3f1df4e02133b26b69dcbdb;hb=21d7606604dab27e62ed700a39425b983901cef1;hp=bfb11832f3e980656d9fb5fe09dc9654aa5f9e2b;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index bfb1183..077ace6 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,112 +1,138 @@
+ * 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
+JPred 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.
-
- -
- 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.
-
-
+ 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.
+ - 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 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.
+