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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/>.
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90 <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
93 <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
96 <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
99 <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
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150 <p>Jalview comes in two distinct flavours.<br>
152 The main application allows connection to multiple web services provided
153 at the University of Dundee as well as a host of additional useful features
154 such as printing, making images from your alignment and annotating your
155 alignment. You need to download and install this software.</p>
156 <p>The applet version runs in web browsers and is a useful interactive
157 display for precalculated alignments, features and annotations files.
158 It does not have the full functionality of the main application, such
159 as making images, saving files, running web service jobs due to security
160 restrictions imposed on applets.</p>
161 <p align="left">For more information on how to use the applet in your
162 website, see <a href="appletParameters.html"><strong>full list of applet
163 parameters.</strong></a></p>
164 <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
165 of Jalview, which runs within your web browser. </p>
166 <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
168 (15 sequences x 150 residues)</H4>
169 <div align="center"> </div>
171 <table width="300" border="1" cellspacing="0" cellpadding="0">
173 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
175 <td width="100"> <applet code="jalview.bin.JalviewLite"
176 width="140" height="35"
177 archive="jalviewApplet.jar">
178 <param name="file" value="uniref50.fa">
179 <param name="treeFile" value="ferredoxin.nw">
180 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
181 <param name="showFullId" value="false">
182 <param name="RGB" value="F2F2FF">
183 <param name="sortByTree" value="True">
184 <param name="showSequenceLogo" value="true">
185 <param name="showGroupConsensus" value="true">
186 <param name="linkLabel_1" value="SRS">
187 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
188 <param name="linkLabel_2" value="Uniprot">
189 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
190 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
192 <td width="165">User Defined Colours, loads an associated Newick
193 format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
199 <table width="300" border="1" cellspacing="0" cellpadding="0">
201 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
203 <td width="100"> <applet code="jalview.bin.JalviewLite"
204 width="140" height="35"
205 archive="jalviewApplet.jar">
206 <param name="file" value="uniref50.fa">
207 <param name="features" value="exampleFeatures.txt">
208 <param name="showFeatureSettings" value="true">
209 <param name="wrap" value="true">
210 <param name="showAnnotation" value="false">
211 <param name="windowHeight" value="500">
212 <param name="windowWidth" value="650">
213 <param name="showFullId" value="false">
214 <param name="RGB" value="F2F2FF">
215 <param name="linkLabel_1" value="SRS">
216 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
217 <param name="linkLabel_2" value="Uniprot">
218 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
219 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
221 <td width="165">Displays a features file on the alignment</td>
227 <table width="300" border="1" cellspacing="0" cellpadding="0">
229 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
231 <td width="100"> <applet code="jalview.bin.JalviewLite"
232 width="140" height="35"
233 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
234 <param name="file" value="uniref50.fa">
235 <!-- <param name="debug" value="true">
237 <param name="defaultColour" value="Strand Propensity">
238 <param name="wrap" value="true">
239 <param name="showAnnotation" value="false">
240 <param name="windowHeight" value="500">
241 <param name="windowWidth" value="650">
242 <param name="showFullId" value="false">
243 <param name="RGB" value="F2F2FF">
244 <param name="linkLabel_1" value="SRS">
245 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
246 <param name="linkLabel_2" value="Uniprot">
247 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
248 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
249 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
251 <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
257 <table width="300" border="1" cellspacing="0" cellpadding="0">
259 <td><table width="300" border="0" cellspacing="0"
262 <td width="100"><applet code="jalview.bin.JalviewLite"
263 width="140" height="35" archive="jalviewApplet.jar">
264 <param name="file" value="jpred_msa.fasta">
265 <param name="jnetfile" value="jpred_msa.seq.concise">
266 <param name="defaultColour" value="Clustal">
267 <param name="showAnnotation" value="true">
268 <param name="windowHeight" value="515">
269 <param name="windowWidth" value="650">
270 <param name="showConservation" value="false">
271 <param name="showQuality" value="false">
272 <param name="showConsensus" value="false">
273 <param name="showFullId" value="false">
274 <param name="RGB" value="F2F2FF">
275 <param name="linkLabel_1" value="SRS">
276 <param name="linkUrl_1"
277 value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
278 <param name="linkLabel_2" value="Uniprot">
279 <param name="linkUrl_2"
280 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
281 <param name="APPLICATION_URL"
282 value="http://www.jalview.org/services/launchApp">
284 <td width="165">Displays a Multiple Sequence Alignment
285 Based JNet Prediction for a Sequence</td>
291 <table width="300" border="1" cellspacing="0" cellpadding="0">
293 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
295 <td width="100"> <applet code="jalview.bin.JalviewLite"
296 width="140" height="35"
297 archive="jalviewApplet.jar">
298 <param name="file" value="RF00031_folded.stk">
299 <param name="defaultColour" value="Purine/Pyrimidine">
300 <param name="showAnnotation" value="true">
301 <param name="windowHeight" value="515">
302 <param name="windowWidth" value="650">
303 <param name="showConservation" value="false">
304 <param name="showQuality" value="false">
305 <param name="showConsensus" value="true">
306 <param name="showFullId" value="false">
307 <param name="RGB" value="F2F2FF">
308 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
310 <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
317 <p>For more JalviewLite examples, follow the links below.
319 <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
320 <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
321 <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
322 <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
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