From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 16 Sep 2013 15:06:57 +0000 (+0100)
Subject: Add info on new programs
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8b5d2d277a9d60d99390da304de9346686952468;p=jabaws.git

Add info on new programs
---

diff --git a/website/index.html b/website/index.html
index eca1691..4dd5d80 100644
--- a/website/index.html
+++ b/website/index.html
@@ -47,9 +47,10 @@ is free software which provides <a href="http://en.wikipedia.org/wiki/Web_servic
 include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, 
 <a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, 
 <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. Analysis services allow
-prediction of protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, 
+prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, 
 <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> and <a href="http://globplot.embl.de/">GlobPlot</a>; 
-and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>.  
+and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The secondary structure for an RNA aligment is possible with 
+the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
 </p><p> 
 <span style="color:black; font-weight:normal; text-align:left;">
 JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment 
diff --git a/website/man_about.html b/website/man_about.html
index a1c5375..46a7134 100644
--- a/website/man_about.html
+++ b/website/man_about.html
@@ -112,6 +112,11 @@
   <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
 </ul>
+<p>Protein Secondary structure</p>
+<ul>
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/www-jpred">Jpred</a></span> (3.0.3) </li>
+</ul>
+
 <p>Protein disorder prediction</p>
 <ul>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>
@@ -119,10 +124,14 @@
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>
   </ul>
-<p>Amino Acid conservation </p>
+<p>Amino Acid conservation</p>
 <ul>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>
 </ul>
+<p>Secondary structure for an RNA aligment</p>
+<ul>
+  <li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>
+</ul>