Add reference on Jronn

[jabaws.git] / website / man_about.html

diff --git a/website/man_about.html b/website/man_about.html
index 55cdc98..2c72efc 100644 (file)
--- a/website/man_about.html
+++ b/website/man_about.html
@@ -18,7 +18,7 @@
 <table>\r
   <tr>\r
     <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-    <td class="bg"><img src="images/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.1" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+    <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
     <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
   </tr>\r
 </table>\r
@@ -59,7 +59,7 @@
   <li><a href="#wisjaba">What is JABAWS?</a></li>\r
   <li><a href="#wjaba">JABAWS Benefits</a></li>\r
   <li><a href="#alprog">JABA Web Services Programs </a></li>\r
-  <li><a href="#jaba2.0.1">What is new in JABAWS 2?</a> </li>\r
+  <li><a href="#jaba2.1">What is new in JABAWS 2.1?</a> </li>\r
   <li><a href="#jabaclient">What is JABAWS Client</a>?</li>\r
   <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>\r
   <li><a href="#cmdclient">Programmatic access to JABAWS</a></li>\r
@@ -106,28 +106,37 @@
 <p>Multiple Sequence Alignement </p>\r
 <ul>\r
   <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
-  <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.0.12)</li>\r
+  <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
   <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
   <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
   <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
 </ul>\r
+<p>Protein Secondary structure prediction</p>\r
+<ul>\r
+  <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>\r
+</ul>\r
+\r
 <p>Protein disorder prediction</p>\r
 <ul>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>\r
-  <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>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;">Jronn - Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>\r
   </ul>\r
-<p>Amino Acid conservation </p>\r
+<p>Amino Acid conservation</p>\r
 <ul>\r
   <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>\r
 </ul>\r
+<p>Secondary structure for an RNA aligment</p>\r
+<ul>\r
+  <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>\r
+</ul>\r
 \r
+All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> section (registration is required).\r
 \r
-\r
-<h3><a name="jaba2.0.1"/></a>What is new in JABAWS 2.0.1? </h3>\r
-<p>JABAWS Version 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>\r
+<h3><a name="jaba2.1"/></a>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong><p>JABAWS 2.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
 <ul>\r
   <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
   <li>Jronn failed to process jobs with more than 3 sequences</li>\r
@@ -171,8 +180,8 @@
 \r
 <h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
 <p>\r
-  JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
-  v2.0 clients should also be able to use JABAWS 2.0.1 services. To access the analysis web services introduced in\r
+  JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
+  v2.0 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in\r
   JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
 </p>\r
 \r