VARNA(1)

💖 VARNA — the NAME energy 💖

varna — Assisted drawing of RNA secondary structure. That's the whole vibe, bestie: it draws your RNA for you, lowkey carrying.

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🌸 SYNOPSIS 🌸

java -cp . [-i InFile|-sequenceDBN XXX -structureDBN YYY] -o OutFile
[Options]

Like, that's the shape of the incantation. 🪄

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🎀 DESCRIPTION 🎀

VARNA v3.9 — Assisted drawing of RNA secondary structure (Command Line version). It's giving "I render your base pairs and I do it beautifully." No cap.

📍 Where: (the two files you gotta know about)

• OutFile — the file you're writing out to. Supported formats: {JPEG,PNG,EPS,XFIG,SVG}
• InFile — your secondary structure file, the one going in. Supported formats: {BPSEQ,CT,RNAML,DBN}

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👑 Main options 👑

• -algorithm — which drawing algorithm to use, pick from [naview,line,radiate,circular]. This is the whole aesthetic choice fr.
• -backbone — backbone color (Ex: #334455)
• -baseInner — default value for inner base color (Ex: #334455)
• -baseOutline — base outline color (Ex: #334455)
• -bp — base pair color (Ex: #334455)
• -bpStyle — the look and feel for how base pairs get drawn, pick from [lw,lwalt,none,simple,rnaviz]
• -h — shows you a short lil description of the main options, then exits. A snack, not a meal. 👋
• -periodNum — periodicity of base-numbering. iykyk.
• -x — shows a detailed description of all the options. The full lore drop.

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🦋 Advanced options 🦋

(this is the deep end, babes — drink water first 💧)

• -annotations — a set of textual annotations
• -applyBasesStyle — base style application
• -autoHelices
• -autoInteriorLoops
• -autoTerminalLoops

Okay so those last few don't have a description in here. Iconic mystery behavior, honestly. They're just standing there being themselves. 🧚

• -auxBPs — adds a list of (possibly non-canonical) base-pairs on top of the ones already defined by your main secondary structure (Ex: "(1,10);(2,11);(3,12)"). You can also give custom BP styles (Ex: "(2,11):thickness=4;(3,12):color=#FF0000").
• -background — background color (Ex: #334455)
• -baseName — residues font color (Ex: #334455)
• -baseNum — base numbers font color (Ex: #334455)
• -basesStyle — base style declaration
• -border — border width and height in pixels (Ex: "20x40")
• -bpIncrement — the distance between nested base-pairs (aka arcs) in the linear representation
• -chemProb
• -colorMap — associates a list of numerical values (eg '0.2,0.4,0.6,0.8') with the RNA bases in their natural order, and changes the color used to fill those bases according to the current color map style.
• -colorMapCaption — sets the current color map caption.
• -colorMapMax
• -colorMapMin
• -colorMapStyle — picks a specific color map style. It can be one of the predefined styles (eg 'red', 'green', 'blue', 'bw', 'heat', 'energy') or a brand new one (eg '0:#FFFF00;1:#ffFFFF;6:#FF0000').
• -columns — sets number of rows
• -comparisonMode — activates comparison mode
• -customBPs
• -customBases
• -drawBackbone — true if the backbone must be drawn, false otherwise
• -drawBases — shows/hides the outline of bases
• -drawColorMap
• -drawNC — toggles on/off the display of non-canonical base-pairs
• -drawTertiary — toggles on/off the display of tertiary interaction, ie pseudoknots
• -error — show errors
• -fillBases — fills or leaves empty the inner portions of bases
• -firstSequence — in comparison mode, the sequence of the first RNA
• -firstStructure — in comparison mode, the structure of the first RNA
• -flat — toggles on/off (true/false) drawing exterior bases on a straight line
• -flip — draws a set of exterior helices, identified by the argument string, in clockwise order (the default drawing is counter-clockwise). The argument is a semicolon-separated list of helices, each one identified by a base or a base-pair (eg. "2;20-34").
• -gapsColor — define and use a custom color for gap bases in comparison mode
• -highlightRegion — highlight a set of contiguous regions
• -modifiable — allows/prohibits modifications
• -nsBasesColor — define and use a custom color for non-standard bases in comparison mode
• -orientation — sets the general orientation of an RNA, i.e. the deviation of the longest axis (defined by the most distant couple of bases) from the horizontal axis.
• -quality — sets quality (non-vector file formats only)
• -resolution — sets resolution (non-vector file formats only)
• -rotation — rotates the RNA after the initial drawing (Ex: '20' for a 20 degree counter-clockwise rotation)
• -rows — sets number of columns
• -secondSequence — in comparison mode, the sequence of the second RNA
• -secondStructure — in comparison mode, the structure of the second RNA
• -sequenceDBN — raw RNA sequence
• -spaceBetweenBases — sets the space between consecutive bases
• -structureDBN — RNA structure given in dot bracket notation (DBN)
• -title — RNA drawing title
• -titleColor — title color (Ex: #334455)
• -titleSize — title font size
• -warning — show warnings
• -zoom — zoom coefficient
• -zoomAmount — zoom increment on user interaction

💀 psst — yes, -columns says it sets the number of rows and -rows says it sets the number of columns. That's what the page says, bestie. I'm just the messenger. 🙈

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And that's the whole page, babe. This one's varna 3-93+ds, dated January 2026 — yes, she's that girl. Go draw something gorgeous. 💅✨🦋🎀🌸🫶