1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
|
<!--
* Jalview - A Sequence Alignment Editor and Viewer (2.11.4.1)
* Copyright (C) 2024 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#applets"> here</a> to view decorated page</b></div>
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
</div>
<!-- content template start -->
<p align="left">
<h2>JalviewLite Button Examples</h2>
Try out JalviewLite by pressing one of the buttons below.
<a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/applets.html">this page</a> and viewing the page source manually).<br/>
For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
<p> </p><div align="center">
<p align="center">
<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,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.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="sortByTree" value="True"/>
<param name="showSequenceLogo" value="true"/>
<param name="showGroupConsensus" value="true"/>
<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="EMBL-EBI Search"/>
<param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
<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,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<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"/>
<param name="linkLabel_1" value="Uniprot"/>
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
<param name="linkLabel_2" value="EMBL-EBI Search"/>
<param name="linkUrl_2"
value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
<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-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<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="debug" value="true"/>
<param name="showAnnotation" value="false"/>
<param name="defaultColour" value="Strand Propensity"/>
<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
<param name="linkLabel_1" value="Uniprot"/>
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
<param name="linkLabel_2" value="EMBL-EBI Search"/>
<param name="linkUrl_2"
value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</td>
<td valign="center">Associates PDB file 1GAQ with sequence
FER1_MAIZE</td>
</tr>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="jpred_msa.fasta"/>
<param name="jnetfile" value="jpred_msa.seq.concise"/>
<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"/>
<param name="linkLabel_1" value="Uniprot"/>
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
<param name="linkLabel_2" value="EMBL-EBI Search"/>
<param name="linkUrl_2"
value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</td>
<td valign="middle">Displays a Multiple Sequence Alignment
Based JPred 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,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<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"/>
<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>
<p>
<h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
</p>
<table width="90%">
<tr>
<td width="10%" valign="center">
<applet
code="jalview.bin.JalviewLite" width="140" height="35"
archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
<param name="file" value="estrogenReceptorProtein_frag.fa"/>
<param name="enableSplitFrame" value="true"/>
<param name="scaleProteinAsCdna" value="true"/>
<param name="showFullId" value="false"/>
<param name="windowHeight" value="300"/>
<param name="windowWidth" value="800"/>
<param name="showAnnotation" value="true"/>
<param name="showSequenceLogo" value="true"/>
<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
<param name="defaultColourProt" value="Clustal"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</td>
<td valign="center">Displays a split window view showing aligned protein
and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
via the Jalview Desktop).<br />Data retrieved from Uniprot and
ENA, after Thornton, Need and Crews, <a
href="http://dx.doi.org/10.1126/science.1086185">Science 19
September 2003: 301 (5640), 1714-1717</a>
</td>
</tr>
</table>
|
