VARNA: plot 2D structure with styles


Command line tools: java and VARNAv3-93.jar (downloadable at VARNA)


Aim:

  • Setup base pair color (#606060) and backbone colors (#000000)
  • Setup the resolution of the bitmap to 5.0
  • Save the plot to Plot.png

Command:

java -cp ./VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "GUCUUAUUACACACAGUCAAUGAGCCCGUUCCAAGUCCGUUUGGGCAC" -structureDBN "(((.(((.((.....))..))).)))...(((((......)))))..." -bp "#606060" -backbone "#000000" -o Plot.png -resolution "5.0"

Plot:

WESTERLIES


Aim:

  • Use VARNA GUI
  • Hide the outline of bases
  • Setup inner base color (#FFFFFF)
  • Change space between bases to 0.57
  • Hide backbone
  • Use simple base pairing style

Command:

java -cp ./VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "GUCUUAUUACACACAGUCAAUGAGGCCCGUUCCAAGUCCGUUUGGGCGAC" -structureDBN "(((.(((.((.....))..))).)))....(((((......)))))...." -bp "#606060" -backbone "#000000" -drawBases False -baseInner "#FFFFFF" -spaceBetweenBases "0.57" -drawBackbone False -bpStyle simple

Plot:

WESTERLIES


Aim:

  • Highlight bases 5-10 using custom outline (#db240f)

Command:

java -cp ./VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "GUCUUAUUACACACAGUCAAUGAGGCCCGUUCCAAGUCCGUUUGGGCGAC" -structureDBN "(((.(((.((.....))..))).)))....(((((......)))))...." -bp "#606060" -backbone "#000000" -drawBases False -baseInner "#FFFFFF" -spaceBetweenBases "0.57" -drawBackbone False -bpStyle simple -highlightRegion "5-22:radius=10,fill=#db240f,outline=#db240f;" -resolution "5.0"

Plot:

WESTERLIES


Aim:

  • Use a custom base style for bases 35-42 (#00ebff)

Command:

java -cp ./VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "GUCUUAUUACACACAGUCAAUGAGGCCCGUUCCAAGUCCGUUUGGGCGAC" -structureDBN "(((.(((.((.....))..))).)))....(((((......)))))...." -bp "#606060" -backbone "#000000" -drawBases False -baseInner "#FFFFFF" -spaceBetweenBases "0.57" -drawBackbone False -bpStyle simple  -basesStyle1 "outline=#000000,label=#000000,fill=#00ebff" -applyBasesStyle1on "35-42"

Plot:

WESTERLIES


Aim:

  • Use custom color map rendering to the bases (#f5f5f5 to #f50000)

Command:

java -cp ./VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "GUCUUAUUACACACAGUCAAUGAGGCCCGUUCCAAGUCCGUUUGGGCGAC" -structureDBN "(((.(((.((.....))..))).)))....(((((......)))))...." -bp "#606060" -backbone "#000000" -drawBases False -baseInner "#FFFFFF" -spaceBetweenBases "0.57" -drawBackbone False -bpStyle simple -colorMapStyle "0:#f5f5f5;1:#f50000" -colorMap "0.7;0.8;0.2;1.0;1.0;1.0;0.0;1.0;1.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;1.0;1.0;1.0;1.0;1.0;0.5;0.5;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.5;1.0;0.5;0.0;0.0;0.0;1.0;0.0;0.0;1.0;0.0;0.5;1.0;1.0;0.5;1.0;1.0;1.0;"

Plot:

WESTERLIES


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