JNet Secondary Structure Prediction

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=e42a4e6943e4d64f4c472fbb029800381f4cbef8;hb=57db03ae9b6b80c19901d604b376b41f6fbab31a;hp=8b0557f70e6ea97ac58f4fdab856603992009e19;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 8b0557f..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 @@ -52,35 +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 @@ -96,9 +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.
@@ -112,25 +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. - 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.