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3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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8 * Jalview is free software: you can redistribute it and/or
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15 * PURPOSE. See the GNU General Public License for more details.
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147 <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
148 <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
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166 Working on Snow Leopard or Java out of date ? Try <a href="u_applets.html">the unsigned applet demos</a>
170 <!-- content template start -->
173 <h2>JalviewLite Button Examples</h2>
174 Try out JalviewLite by pressing one of the buttons below.<br/>
175 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>
178 <h2>Ferredoxins, chloroplast precursor related UniRef50
180 <br /> (15 sequences x 150 residues)
184 <td width="10%" valign="center">
186 code="jalview.bin.JalviewLite" width="140" height="35"
187 archive="jalviewApplet.jar">
188 <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="sortByTree" value="True"/><param name="showSequenceLogo" value="true"/><param name="showGroupConsensus" value="true"/><param name="showFullId" value="false"/>
189 <param name="linkLabel_1" value="Uniprot"/>
190 <param name="linkUrl_1"
191 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
192 <param name="linkLabel_2" value="EMBL-EBI Search"/>
193 <param name="linkUrl_2"
194 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
195 <param name="APPLICATION_URL"
196 value="http://www.jalview.org/services/launchApp"/>
199 <td valign="center">User Defined Colours, loads an associated
200 Newick format tree file which is used to sort the alignment, and
201 group consensus and sequence logos are shown below the alignment.</td>
204 <td width="10%" valign="center"><applet
205 code="jalview.bin.JalviewLite" width="140" height="35"
206 archive="jalviewApplet.jar">
207 <param name="file" value="uniref50.fa"/><param name="features" value="exampleFeatures.txt"/><param name="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="showFeatureSettings" value="true"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/>
208 <param name="linkLabel_1" value="Uniprot"/>
209 <param name="linkUrl_1"
210 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
211 <param name="linkLabel_2" value="EMBL-EBI Search"/>
212 <param name="linkUrl_2"
213 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
214 <param name="APPLICATION_URL"
215 value="http://www.jalview.org/services/launchApp"/>
218 <td valign="center">Displays a features file on the alignment</td>
221 <td width="10%" valign="center"><applet
222 code="jalview.bin.JalviewLite" width="140" height="35"
223 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
224 <param name="file" value="uniref50.fa"/><param name="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/><param name="defaultColour" value="Strand Propensity"/>
225 <param name="linkLabel_1" value="Uniprot"/>
226 <param name="linkUrl_1"
227 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
228 <param name="linkLabel_2" value="EMBL-EBI Search"/>
229 <param name="linkUrl_2"
230 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
231 <param name="APPLICATION_URL"
232 value="http://www.jalview.org/services/launchApp"/>
235 <td valign="center">Associates PDB file 1GAQ with sequence
239 <td width="10%" valign="center"><applet
240 code="jalview.bin.JalviewLite" width="140" height="35"
241 archive="jalviewApplet.jar">
242 <param name="file" value="jpred_msa.fasta"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Clustal"/>
243 <param name="linkLabel_1" value="Uniprot"/>
244 <param name="linkUrl_1"
245 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
246 <param name="linkLabel_2" value="EMBL-EBI Search"/>
247 <param name="linkUrl_2"
248 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
249 <param name="APPLICATION_URL"
250 value="http://www.jalview.org/services/launchApp"/>
253 <td valign="middle">Displays a Multiple Sequence Alignment
254 Based JNet Prediction for a Sequence</td>
258 <h2>RF00031 RFAM Alignment with per sequence secondary
263 <td width="10%" valign="center"><applet
264 code="jalview.bin.JalviewLite" width="140" height="35"
265 archive="jalviewApplet.jar">
266 <param name="file" value="RF00031_folded.stk"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Purine/Pyrimidine"/>
267 <param name="APPLICATION_URL"
268 value="http://www.jalview.org/services/launchApp"/>
271 <td valign="center">Displays an RFAM RNA fold family with
272 secondary structure annotation</td>
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286 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
289 If you use Jalview in your work, please cite this publication:
293 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
294 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
295 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>