<param name="windowHeight" value="500"/>
<param name="windowWidth" value="650"/>
<param name="wrap" value="true"/>
+<param name="debug" value="true"/>
<param name="showAnnotation" value="false"/>
<param name="defaultColour" value="Strand Propensity"/>
<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
code="jalview.bin.JalviewLite" width="140" height="35"
archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
-<param name="file" value="estrogenReceptorCdna.fa"/>
-<param name="file2" value="estrogenReceptorProtein.fa"/>
+<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
+<param name="file" value="estrogenReceptorProtein_frag.fa"/>
<param name="enableSplitFrame" value="true"/>
<param name="scaleProteinAsCdna" value="true"/>
<param name="showFullId" value="false"/>
<param name="windowWidth" value="800"/>
<param name="showAnnotation" value="true"/>
<param name="showSequenceLogo" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</td>
- <td valign="center">Displays a split window view of protein
- and its related cDNA.<br />Data retrieved from Uniprot and ENA,
- after Thornton, Need and Crews, <a
+ <td valign="center">Displays a split window view showing aligned protein
+ and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
+ href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
+ via the Jalview Desktop).<br />Data retrieved from Uniprot and
+ ENA, after Thornton, Need and Crews, <a
href="http://dx.doi.org/10.1126/science.1086185">Science 19
September 2003: 301 (5640), 1714-1717</a>
</td>