====== What's VARNA ======
  * [[http://varna.lri.fr | VARNA]] is Java lightweight Applet dedicated to drawing the secondary structure of RNA

====== Installation ======
  * Download the software from [[http://varna.lri.fr/index.php?lang=en&page=downloads&css=varna | this site]]
  * Install java JRE from [[https://www.java.com/en/download/ | this site]]
====== How to use it ======
=====Command-line mode=====


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  * 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…
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  * Black background: run the following script
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<code>
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'\
     
</code>
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{{:wyj:varna_b.png?130|}}
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  * White background: run the following script
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<code>
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'\


</code>
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{{:wyj:varna_w.png?130|}}
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* For more options, please refer to [[http://varna.lri.fr/index.php?lang=en&css=varna&page=command | the command page ]]



=====GUI mode=====
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  * Adding below command to your cshrc using alias syntax
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<code>
java -cp /home/avalon007/codelib/cmd/Varna/VARNAv3-93-src.jar fr.orsay.lri.varna.applications.VARNAcmd
</code>
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{{ :varna_gui.png|}}
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 * Other unusual notations are also workable such as "&", "[", "{" representing double strands and pesudoknots. 
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