Table of Contents

What's VARNA

Installation

How to use it

Command-line mode

  • 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…
  • Black background: run the following script
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'\

  • White background: run the following script
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'\

* For more options, please refer to the command page

GUI mode

  • Adding below command to your cshrc using alias syntax
java -cp /home/avalon007/codelib/cmd/Varna/VARNAv3-93-src.jar fr.orsay.lri.varna.applications.VARNAcmd

* Other unusual notations are also workable such as “&”, “[”, “{” representing double strands and pesudoknots.