JNet Secondary Structure Prediction

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=9b715c2e8f81a5fe0a12fcde06ccff7a5bbd1fec;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=93c13d89af276b1cefec2788499a49ac6a0f9d69;hpb=c30bcb5bc195374ef89916a1c39e4812fa93bf4c;p=jalview.git diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 93c13d8..9b715c2 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -1,85 +1,117 @@ + 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 prediction methods 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 JNet method uses several different neural networks and decides on +the most likely prediction via a jury network.

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

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:

-The function available from the Calculations→Web -Service→JNet... 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 -that was first clicked on). -
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:

+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 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:

-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.
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.

+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 +JABAWS Jnet service. +