JNet Secondary Structure Prediction

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fjnet.html;h=396a3a7c0d436523688127aedcc8ce12ee60295f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=300982312efa611fcc0992b719ff0a847e23e614;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 3009823..396a3a7 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -1,116 +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 -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.

-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. + 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 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→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.

+ JNet 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 + legacy Jalview SOAP service, and will be replaced in the near future + by a JPred4 Rest service.