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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 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">
33 <param name="treeFile" value="ferredoxin.nw">
34 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
35 <param name="showFullId" value="false">
36 <param name="RGB" value="F2F2FF">
37 <param name="linkLabel_1" value="SRS">
38 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
39 <param name="linkLabel_2" value="Uniprot">
40 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
41 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
43 <td width="165">User Defined Colours, loads an associated Newick
50 <table width="300" border="1" cellspacing="0" cellpadding="0">
52 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
54 <td width="100"> <applet code="jalview.bin.JalviewLite"
55 width="140" height="35"
56 archive="jalviewApplet.jar">
57 <param name="file" value="uniref50.fa">
58 <param name="features" value="exampleFeatures.txt">
59 <param name="showFeatureSettings" value="true">
60 <param name="wrap" value="true">
61 <param name="showAnnotation" value="false">
62 <param name="windowHeight" value="500">
63 <param name="windowWidth" value="650">
64 <param name="showFullId" value="false">
65 <param name="RGB" value="F2F2FF">
66 <param name="linkLabel_1" value="SRS">
67 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
68 <param name="linkLabel_2" value="Uniprot">
69 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
70 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
72 <td width="165">Displays a features file on the alignment</td>
78 <table width="300" border="1" cellspacing="0" cellpadding="0">
80 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
82 <td width="100"> <applet code="jalview.bin.JalviewLite"
83 width="140" height="35"
84 archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
85 <param name="file" value="uniref50.fa">
86 <param name="defaultColour" value="Strand Propensity">
87 <param name="wrap" value="true">
88 <param name="showAnnotation" value="false">
89 <param name="windowHeight" value="500">
90 <param name="windowWidth" value="650">
91 <param name="showFullId" value="false">
92 <param name="RGB" value="F2F2FF">
93 <param name="linkLabel_1" value="SRS">
94 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
95 <param name="linkLabel_2" value="Uniprot">
96 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
97 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
98 <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
100 <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
106 <table width="300" border="1" cellspacing="0" cellpadding="0">
108 <td><table width="300" border="0" cellspacing="0" cellpadding="0">
110 <td width="100"> <applet code="jalview.bin.JalviewLite"
111 width="140" height="35"
112 archive="jalviewApplet.jar">
113 <param name="file" value="jpred_msa.fasta">
114 <param name="jnetfile" value="jpred_msa.seq.concise">
115 <param name="defaultColour" value="Clustal">
116 <param name="showAnnotation" value="true">
117 <param name="windowHeight" value="515">
118 <param name="windowWidth" value="650">
119 <param name="showConservation" value="false">
120 <param name="showQuality" value="false">
121 <param name="showConsensus" value="false">
122 <param name="showFullId" value="false">
123 <param name="RGB" value="F2F2FF">
124 <param name="linkLabel_1" value="SRS">
125 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
126 <param name="linkLabel_2" value="Uniprot">
127 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
128 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
130 <td width="165">Displays a Multiple Sequence Alignment Based
131 JNet Prediction for a Sequence</td>
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