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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.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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147 <li class="jvlite-nav-small"><a href="u_applets.html">JalviewLite Examples</a></li>
148 <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
149 <li ><a href="u_appletParameters.html">Applet Parameters</a></li>
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166 Scary Java warnings ? Try <a href="applets.html">the signed 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="u_jalviewApplet.jar">
188 <param name="file" value="uniref50.fa"/>
189 <param name="treeFile" value="ferredoxin.nw"/>
190 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
191 <param name="sortByTree" value="True"/>
192 <param name="showSequenceLogo" value="true"/>
193 <param name="showGroupConsensus" value="true"/>
194 <param name="showFullId" value="false"/>
195 <param name="linkLabel_1" value="Uniprot"/>
196 <param name="linkUrl_1"
197 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
198 <param name="linkLabel_2" value="EMBL-EBI Search"/>
199 <param name="linkUrl_2"
200 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
201 <param name="APPLICATION_URL"
202 value="http://www.jalview.org/services/launchApp"/>
205 <td valign="center">User Defined Colours, loads an associated
206 Newick format tree file which is used to sort the alignment, and
207 group consensus and sequence logos are shown below the alignment.</td>
210 <td width="10%" valign="center"><applet
211 code="jalview.bin.JalviewLite" width="140" height="35"
212 archive="u_jalviewApplet.jar">
213 <param name="file" value="uniref50.fa"/>
214 <param name="features" value="exampleFeatures.txt"/>
215 <param name="showFullId" value="false"/>
216 <param name="windowHeight" value="500"/>
217 <param name="windowWidth" value="650"/>
218 <param name="showFeatureSettings" value="true"/>
219 <param name="wrap" value="true"/>
220 <param name="showAnnotation" value="false"/>
221 <param name="linkLabel_1" value="Uniprot"/>
222 <param name="linkUrl_1"
223 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
224 <param name="linkLabel_2" value="EMBL-EBI Search"/>
225 <param name="linkUrl_2"
226 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
227 <param name="APPLICATION_URL"
228 value="http://www.jalview.org/services/launchApp"/>
231 <td valign="center">Displays a features file on the alignment</td>
234 <td width="10%" valign="center"><applet
235 code="jalview.bin.JalviewLite" width="140" height="35"
236 archive="u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar">
237 <param name="file" value="uniref50.fa"/>
238 <param name="showFullId" value="false"/>
239 <param name="windowHeight" value="500"/>
240 <param name="windowWidth" value="650"/>
241 <param name="wrap" value="true"/>
242 <param name="showAnnotation" value="false"/>
243 <param name="defaultColour" value="Strand Propensity"/>
244 <param name="linkLabel_1" value="Uniprot"/>
245 <param name="linkUrl_1"
246 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
247 <param name="linkLabel_2" value="EMBL-EBI Search"/>
248 <param name="linkUrl_2"
249 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
250 <param name="APPLICATION_URL"
251 value="http://www.jalview.org/services/launchApp"/>
254 <td valign="center">Associates PDB file 1GAQ with sequence
258 <td width="10%" valign="center"><applet
259 code="jalview.bin.JalviewLite" width="140" height="35"
260 archive="u_jalviewApplet.jar">
261 <param name="file" value="jpred_msa.fasta"/>
262 <param name="showFullId" value="false"/>
263 <param name="windowHeight" value="515"/>
264 <param name="windowWidth" value="650"/>
265 <param name="showAnnotation" value="true"/>
266 <param name="defaultColour" value="Clustal"/>
267 <param name="linkLabel_1" value="Uniprot"/>
268 <param name="linkUrl_1"
269 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
270 <param name="linkLabel_2" value="EMBL-EBI Search"/>
271 <param name="linkUrl_2"
272 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
273 <param name="APPLICATION_URL"
274 value="http://www.jalview.org/services/launchApp"/>
277 <td valign="middle">Displays a Multiple Sequence Alignment
278 Based JNet Prediction for a Sequence</td>
282 <h2>RF00031 RFAM Alignment with per sequence secondary
287 <td width="10%" valign="center"><applet
288 code="jalview.bin.JalviewLite" width="140" height="35"
289 archive="u_jalviewApplet.jar">
290 <param name="file" value="RF00031_folded.stk"/>
291 <param name="showFullId" value="false"/>
292 <param name="windowHeight" value="515"/>
293 <param name="windowWidth" value="650"/>
294 <param name="showAnnotation" value="true"/>
295 <param name="defaultColour" value="Purine/Pyrimidine"/>
296 <param name="APPLICATION_URL"
297 value="http://www.jalview.org/services/launchApp"/>
300 <td valign="center">Displays an RFAM RNA fold family with
301 secondary structure annotation</td>
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315 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
318 If you use Jalview in your work, please cite this publication:
322 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
323 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
324 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>