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4 <p>Jalview comes in two distinct flavours.<br>
6 The main application allows connection to multiple web services provided
7 at the University of Dundee as well as a host of additional useful features
8 such as printing, making images from your alignment and annotating your
9 alignment. You need to download and install this software.</p>
10 <p>The applet version runs in web browsers and is a useful interactive
11 display for precalculated alignments, features and annotations files.
12 It does not have the full functionality of the main application, such
13 as making images, saving files, running web service jobs due to security
14 restrictions imposed on applets.</p>
15 <p align="left">For more information on how to use the applet in your
16 website, see <a href="appletParameters.html"><strong>full list of applet
17 parameters.</strong></a></p>
18 <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
19 of Jalview, which runs within your web browser. </p>
20 <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
22 (15 sequences x 150 residues)</H4>
23 <div align="center"> </div>
25 <table width="300" border="1" cellspacing="0" cellpadding="0">
27 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
29 <td width="100"> <applet code="jalview.bin.JalviewLite"
30 width="140" height="35"
31 archive="jalviewApplet.jar">
32 <param name="file" value="uniref50.fa">
\r <param name="treeFile" value="ferredoxin.nw">
33 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
34 <param name="showFullId" value="false">
35 <param name="RGB" value="F2F2FF">
\r <param name="sortByTree" value="True">
\r <param name="showSequenceLogo" value="true">
\r <param name="showGroupConsensus" value="true">
\r <param name="linkLabel_1" value="SRS">
36 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
37 <param name="linkLabel_2" value="Uniprot">
38 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
39 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
41 <td width="165">User Defined Colours, loads an associated Newick
42 format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
48 <table width="300" border="1" cellspacing="0" cellpadding="0">
50 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
52 <td width="100"> <applet code="jalview.bin.JalviewLite"
53 width="140" height="35"
54 archive="jalviewApplet.jar">
55 <param name="file" value="uniref50.fa">
56 <param name="features" value="exampleFeatures.txt">
57 <param name="showFeatureSettings" value="true">
58 <param name="wrap" value="true">
59 <param name="showAnnotation" value="false">
60 <param name="windowHeight" value="500">
61 <param name="windowWidth" value="650">
62 <param name="showFullId" value="false">
63 <param name="RGB" value="F2F2FF">
64 <param name="linkLabel_1" value="SRS">
65 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
66 <param name="linkLabel_2" value="Uniprot">
67 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
68 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
70 <td width="165">Displays a features file on the alignment</td>
76 <table width="300" border="1" cellspacing="0" cellpadding="0">
78 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
80 <td width="100"> <applet code="jalview.bin.JalviewLite"
81 width="140" height="35"
82 archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
83 <param name="file" value="uniref50.fa">
\r <!-- <param name="debug" value="true">
84 -->
\r <param name="defaultColour" value="Strand Propensity">
85 <param name="wrap" value="true">
86 <param name="showAnnotation" value="false">
87 <param name="windowHeight" value="500">
88 <param name="windowWidth" value="650">
89 <param name="showFullId" value="false">
90 <param name="RGB" value="F2F2FF">
91 <param name="linkLabel_1" value="SRS">
92 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
93 <param name="linkLabel_2" value="Uniprot">
94 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
95 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
96 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
98 <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
104 <table width="300" border="1" cellspacing="0" cellpadding="0">
106 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
108 <td width="100"> <applet code="jalview.bin.JalviewLite"
109 width="140" height="35"
110 archive="jalviewApplet.jar">
111 <param name="file" value="jpred_msa.fasta">
112 <param name="jnetfile" value="jpred_msa.seq.concise">
113 <param name="defaultColour" value="Clustal">
114 <param name="showAnnotation" value="true">
115 <param name="windowHeight" value="515">
116 <param name="windowWidth" value="650">
117 <param name="showConservation" value="false">
118 <param name="showQuality" value="false">
119 <param name="showConsensus" value="false">
120 <param name="showFullId" value="false">
121 <param name="RGB" value="F2F2FF">
122 <param name="linkLabel_1" value="SRS">
123 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
124 <param name="linkLabel_2" value="Uniprot">
125 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
126 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
128 <td width="165">Displays a Multiple Sequence Alignment Based
129 JNet Prediction for a Sequence</td>
133 </table>
\r </div>
\r <p> </p>
\r <p>For more JalviewLite examples, follow the links below.
\r <ul>
\r <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
\r <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
\r <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
\r <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
\r </ul>
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