-<ul>
- <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
- FASTA format</li>
- <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
- Format Sequence Features file</li>
- <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
- Jalview Alignment Annotations File</li>
-</ul>
-<applet code="jalview.bin.JalviewLite"
- width="756" height="560" archive="jalviewApplet.jar">
- <param name="file" value="plantfdx.fa">
- <param name="annotations" value="plantfdx.annotations">
- <param name="features" value="plantfdx.features">
- <param name="embedded" value="true">
- <param name="userDefinedColour"
- value="C=yellow; R,K,H=FF5555; D,E=5555FF">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1"
- value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet>
+ <ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+ </ul>
+ <applet
+ code="jalview.bin.JalviewLite" width="756" height="560"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="features" value="plantfdx.features"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="showFullId" value="false"/>
+<param name="embedded" value="true"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</p>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>