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+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
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+ <a href="http://www.jalview.org/development/release-history">Release History</a>
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+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
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</div>
-<div id="pageWrap">
+ <div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li class="jvlite-nav-title"><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
-</ul>
-</div>
+ <div id="sideNav">
+ <ul>
+ <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
+ Examples</a></li>
+ <li><a href="appletParameters.html">Applet Parameters</a></li>
+ <li><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li><a href="formComplete.html">in-page API demo</a></li>
+ <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+ <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+ </ul>
+ </div>
-<div id="content" class="content">
- <p>JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page. It's one of the easiest ways of providing an interactive
- display for precalculated alignments, features and annotations files.
- It lacks some functionality available in the Jalview Desktop, however, such
- as making images, saving files, and running web service jobs. This is mostly due to security
- restrictions imposed on applets.</p>
- <p align="left">For more information on how to use the applet in your
- website, see <a href="appletParameters.html"><strong>full list of applet
- parameters.</strong></a></p>
- <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
- of Jalview, which runs within your web browser. </p>
- <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
- cluster<br>
- (15 sequences x 150 residues)</H4>
- <div align="center"> </div>
- <div align="center">
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
- <param name="treeFile" value="ferredoxin.nw">
- <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="sortByTree" value="True">
- <param name="showSequenceLogo" value="true">
- <param name="showGroupConsensus" value="true">
- <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></td>
- <td width="165">User Defined Colours, loads an associated Newick
- format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
- <param name="features" value="exampleFeatures.txt">
- <param name="showFeatureSettings" value="true">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <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> </td>
- <td width="165">Displays a features file on the alignment</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
- <param name="file" value="uniref50.fa">
- <!-- <param name="debug" value="true">
+ <div id="content" class="content">
+ <p>JalviewLite is a web based version of Jalview, which runs as a
+ Java applet in or on a web page. It's one of the easiest ways of
+ providing an interactive display for precalculated alignments,
+ features and annotations files. It lacks some functionality
+ available in the Jalview Desktop, however, such as making images,
+ saving files, and running web service jobs. This is mostly due to
+ security restrictions imposed on applets.</p>
+ <p align="left">
+ Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
+ href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+ <div align="center">
+ <p>
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <param name="treeFile" value="ferredoxin.nw">
+ <param name="userDefinedColour"
+ value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+ <param name="showFullId" value="false">
+ <param name="sortByTree" value="True">
+ <param name="showSequenceLogo" value="true">
+ <param name="showGroupConsensus" 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="Expasy">
+ <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></td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <param name="features" value="exampleFeatures.txt">
+ <param name="showFeatureSettings" value="true">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <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></td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <!-- <param name="debug" value="true">
-->
- <param name="defaultColour" value="Strand Propensity">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <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">
- <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
- </applet> </td>
- <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0"
- cellpadding="0">
- <tr>
- <td width="100"><applet code="jalview.bin.JalviewLite"
- width="140" height="35" archive="jalviewApplet.jar">
- <param name="file" value="jpred_msa.fasta">
- <param name="jnetfile" value="jpred_msa.seq.concise">
- <param name="defaultColour" value="Clustal">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="false">
- <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></td>
- <td width="165">Displays a Multiple Sequence Alignment
- Based JNet Prediction for a Sequence</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="RF00031_folded.stk">
- <param name="defaultColour" value="Purine/Pyrimidine">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="true">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- </applet> </td>
- <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
- </tr>
- </table></td>
- </tr>
- </table>
- </div>
- <p> </p>
- <p>For more JalviewLite examples, follow the links below.
- <ul>
- <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
- <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
- <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
- <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
- </ul>
-</div>
+ <param name="defaultColour" value="Strand Propensity">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <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">
+ <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+ </applet></td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="middle"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="jpred_msa.fasta">
+ <param name="jnetfile" value="jpred_msa.seq.concise">
+ <param name="defaultColour" value="Clustal">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="false">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <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></td>
+ <td valign="center">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="RF00031_folded.stk">
+ <param name="defaultColour" value="Purine/Pyrimidine">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="true">
+ <param name="showFullId" value="false">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ </div>
<div id ="footer">
<div id="innerFooter">
-<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<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>
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 doi: 10.1093/bioinformatics/btp033
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
</p>
</div>
</div>
</div>
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-
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+
git://source.jalview.org / jalview.git / blobdiff