3 Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
4 href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
7 <h2>Ferredoxins, chloroplast precursor related UniRef50
9 <br /> (15 sequences x 150 residues)
13 <td width="10%" valign="center">
14 <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
15 , "treeFile":"ferredoxin.nw"
16 , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
17 , "showFullId":"false"
19 , "showSequenceLogo":"true"
20 , "showGroupConsensus":"true"} prots=true /></td>
21 <td valign="center">User Defined Colours, loads an associated
22 Newick format tree file which is used to sort the alignment, and
23 group consensus and sequence logos are shown below the alignment.</td>
26 <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
28 , "features":"exampleFeatures.txt"
29 , "showFeatureSettings":"true"
31 , "showAnnotation":"false"
32 , "windowHeight":"500"
34 , "showFullId":"false"}/></td>
35 <td valign="center">Displays a features file on the alignment</td>
38 <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
39 , "file":"uniref50.fa"
40 , "defaultColour":"Strand Propensity"
42 , "showAnnotation":"false"
43 , "windowHeight":"500"
45 , "showFullId":"false"
46 , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
47 <td valign="center">Associates PDB file 1GAQ with sequence
51 <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
52 , "file":"jpred_msa.fasta"
53 , "jnetfile":"jpred_msa.seq.concise"
54 , "defaultColour":"Clustal"
55 , "showAnnotation":"true"
56 , "windowHeight":"515"
58 , "showConservation":"false"
59 , "showQuality":"false"
60 , "showConsensus":"false"
61 , "showFullId":"false"} />
63 <td valign="middle">Displays a Multiple Sequence Alignment
64 Based JNet Prediction for a Sequence</td>
68 <h2>RF00031 RFAM Alignment with per sequence secondary
73 <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
74 , "file":"RF00031_folded.stk"
75 , "defaultColour":"Purine/Pyrimidine"
76 , "showAnnotation":"true"
77 , "windowHeight":"515"
79 , "showConservation":"false"
80 , "showQuality":"false"
81 , "showConsensus":"true"
82 , "showFullId":"false"} prots=false /></td>
83 <td valign="center">Displays an RFAM RNA fold family with
84 secondary structure annotation</td>