• This is a shell script (readily available) showing how VARNA command-line version works. Many options are alternative to get your RNA look cool… Two essential parameters are needed if you just want to outline secondary structure briefly, sequenceDBN and sequenceDBN (dot-bracket notation), further, you can polish you RNA through changing background, baseStyle, backbone… shape, color, whatever. Notation is also workable such as baseNum, periodNum…

java -cp ./VARNAv3-93-src.jar fr.orsay.lri.varna.applications.VARNAcmd \
     -sequenceDBN "$1" -structureDBN "$2" -o "$3.eps" \
     -backbone "#000000" -background "#000000" -baseInner "#54FF9F" \
     -periodNum 5 -spaceBetweenBases 0.6 -baseNum "#FFFFFF" -bp "#f53898"\
     -applyBasesStyle1on "$4"  -basesStyle1 "fill=#f53847"\
     -applyBasesStyle2on "$5"  -basesStyle2 "fill=#f9d362"\    
     -resolution "3.0" -zoom 1.5 -border "100X100" \
     -title "$3" -titleSize 9 -titleColor '#FFFFFF'\
     

java -cp ./VARNAv3-93-src.jar fr.orsay.lri.varna.applications.VARNAcmd \
     -sequenceDBN "$1" -structureDBN "$2" -o "$3.eps" \
     -backbone "#000000" -background "#FFFFFF" -baseInner "#54FF9F" \
     -periodNum 5 -spaceBetweenBases 0.6 -baseNum "#000000" -bp "#f53898"\
     -applyBasesStyle1on "$4"  -basesStyle1 "fill=#f53847"\
     -applyBasesStyle2on "$5"  -basesStyle2 "fill=#f9d362"\    
     -resolution "3.0" -zoom 1.5 -border "100X100" \
     -title "$3" -titleSize 9 -titleColor '#000000'\

java -cp /home/avalon007/codelib/cmd/Varna/VARNAv3-93-src.jar fr.orsay.lri.varna.applications.VARNAcmd