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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
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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/>.
20 <TITLE>JalviewLite Examples</TITLE>
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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="appletParameters.html">Applet Parameters</a></li>
150 <li ><a href="u_embedded.html">Embedded Alignment</a></li>
151 <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
152 <li ><a href="u_formComplete.html">Access from Javascript</a></li>
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154 <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
158 <div id="content" class="content">
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164 <div style="width:35%; align:left; float:right;">
165 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
166 Scary Java warnings ?<br/>Try <a href="applets.html">the signed applet demos</a>
168 <div style="margin:8px; padding:10px; align: left;">
169 <p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
174 <!-- content template start -->
177 <h2>JalviewLite Button Examples</h2>
178 Try out JalviewLite by pressing one of the buttons below.<br/>
179 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>
180 <p> </p><div align="center">
182 <h2>Ferredoxins, chloroplast precursor related UniRef50
184 <br /> (15 sequences x 150 residues)
188 <td width="10%" valign="center">
190 code="jalview.bin.JalviewLite" width="140" height="35"
191 archive="u_jalviewApplet.jar">
192 <param name="file" value="uniref50.fa"/>
193 <param name="treeFile" value="ferredoxin.nw"/>
194 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
195 <param name="sortByTree" value="True"/>
196 <param name="showSequenceLogo" value="true"/>
197 <param name="showGroupConsensus" value="true"/>
198 <param name="showFullId" value="false"/>
199 <param name="linkLabel_1" value="Uniprot"/>
200 <param name="linkUrl_1"
201 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
202 <param name="linkLabel_2" value="EMBL-EBI Search"/>
203 <param name="linkUrl_2"
204 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
205 <param name="APPLICATION_URL"
206 value="http://www.jalview.org/services/launchApp"/>
209 <td valign="center">User Defined Colours, loads an associated
210 Newick format tree file which is used to sort the alignment, and
211 group consensus and sequence logos are shown below the alignment.</td>
214 <td width="10%" valign="center"><applet
215 code="jalview.bin.JalviewLite" width="140" height="35"
216 archive="u_jalviewApplet.jar">
217 <param name="file" value="uniref50.fa"/>
218 <param name="features" value="exampleFeatures.txt"/>
219 <param name="showFullId" value="false"/>
220 <param name="windowHeight" value="500"/>
221 <param name="windowWidth" value="650"/>
222 <param name="showFeatureSettings" value="true"/>
223 <param name="wrap" value="true"/>
224 <param name="showAnnotation" value="false"/>
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">Displays a features file on the alignment</td>
238 <td width="10%" valign="center"><applet
239 code="jalview.bin.JalviewLite" width="140" height="35"
240 archive="u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar">
241 <param name="file" value="uniref50.fa"/>
242 <param name="showFullId" value="false"/>
243 <param name="windowHeight" value="500"/>
244 <param name="windowWidth" value="650"/>
245 <param name="wrap" value="true"/>
246 <param name="showAnnotation" value="false"/>
247 <param name="defaultColour" value="Strand Propensity"/>
248 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
249 <param name="linkLabel_1" value="Uniprot"/>
250 <param name="linkUrl_1"
251 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
252 <param name="linkLabel_2" value="EMBL-EBI Search"/>
253 <param name="linkUrl_2"
254 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
255 <param name="APPLICATION_URL"
256 value="http://www.jalview.org/services/launchApp"/>
259 <td valign="center">Associates PDB file 1GAQ with sequence
263 <td width="10%" valign="center"><applet
264 code="jalview.bin.JalviewLite" width="140" height="35"
265 archive="u_jalviewApplet.jar">
266 <param name="file" value="jpred_msa.fasta"/>
267 <param name="showFullId" value="false"/>
268 <param name="windowHeight" value="515"/>
269 <param name="windowWidth" value="650"/>
270 <param name="showAnnotation" value="true"/>
271 <param name="defaultColour" value="Clustal"/>
272 <param name="linkLabel_1" value="Uniprot"/>
273 <param name="linkUrl_1"
274 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
275 <param name="linkLabel_2" value="EMBL-EBI Search"/>
276 <param name="linkUrl_2"
277 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
278 <param name="APPLICATION_URL"
279 value="http://www.jalview.org/services/launchApp"/>
282 <td valign="middle">Displays a Multiple Sequence Alignment
283 Based JNet Prediction for a Sequence</td>
287 <h2>RF00031 RFAM Alignment with per sequence secondary
292 <td width="10%" valign="center"><applet
293 code="jalview.bin.JalviewLite" width="140" height="35"
294 archive="u_jalviewApplet.jar">
295 <param name="file" value="RF00031_folded.stk"/>
296 <param name="showFullId" value="false"/>
297 <param name="windowHeight" value="515"/>
298 <param name="windowWidth" value="650"/>
299 <param name="showAnnotation" value="true"/>
300 <param name="defaultColour" value="Purine/Pyrimidine"/>
301 <param name="APPLICATION_URL"
302 value="http://www.jalview.org/services/launchApp"/>
305 <td valign="center">Displays an RFAM RNA fold family with
306 secondary structure annotation</td>
310 <!-- content template end -->
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319 <div id="innerFooter">
320 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
323 If you use Jalview in your work, please cite this publication:
327 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
328 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
329 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>