From cee65885b13fc0f2d56c1f5df439be1df363e3b1 Mon Sep 17 00:00:00 2001 From: jprocter Date: Sat, 8 Mar 2008 02:51:06 +0000 Subject: [PATCH] correction to Jnet service documentation --- help/html/webServices/jnet.html | 183 +++++++++++++++++++-------------------- 1 file changed, 91 insertions(+), 92 deletions(-) diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 7a6015a..a8727db 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -1,92 +1,91 @@ - - -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.
-

-

-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:

- -

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. This - means that all columns of the alignment, or selection will be submitted - for prediction, not just the visible ones (see hiding columns). -

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:

- -

- - + + +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.
+

+

+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: +

+ +

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: +

+ +

+ + -- 1.7.10.2