<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa" , "treeFile":"ferredoxin.nw" , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF" , "showFullId":"false" , "sortByTree":"True" , "showSequenceLogo":"true" , "showGroupConsensus":"true"} prots=true /> | User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment. |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions", "file":"uniref50.fa" , "features":"exampleFeatures.txt" , "showFeatureSettings":"true" , "wrap":"true" , "showAnnotation":"false" , "windowHeight":"500" , "windowWidth":"650" , "showFullId":"false"}/> | Displays a features file on the alignment |
<@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"uniref50.fa" , "defaultColour":"Strand Propensity" , "wrap":"true" , "showAnnotation":"false" , "windowHeight":"500" , "windowWidth":"650" , "showFullId":"false" , "PDBfile":"1gaq.txt FER1_MAIZE"} /> | Associates PDB file 1GAQ with sequence FER1_MAIZE |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"jpred_msa.fasta" , "jnetfile":"jpred_msa.seq.concise" , "defaultColour":"Clustal" , "showAnnotation":"true" , "windowHeight":"515" , "windowWidth":"650" , "showConservation":"false" , "showQuality":"false" , "showConsensus":"false" , "showFullId":"false"} /> | Displays a Multiple Sequence Alignment Based JNet Prediction for a Sequence |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"RF00031_folded.stk" , "defaultColour":"Purine/Pyrimidine" , "showAnnotation":"true" , "windowHeight":"515" , "windowWidth":"650" , "showConservation":"false" , "showQuality":"false" , "showConsensus":"true" , "showFullId":"false"} prots=false /> | Displays an RFAM RNA fold family with secondary structure annotation |