---
name: "varna"
section: "1"
platform: "linux"
package: "varna"
version: "3-93+ds-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/varna"
---

# varna(1)

Assisted drawing of RNA secondary structure

## NAME

varna - Assisted drawing of RNA secondary structure

## SYNOPSIS

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

## DESCRIPTION

VARNA v3.9 Assisted drawing of RNA secondary structure (Command Line version)

### Where:

- OutFile

  Supported formats: {JPEG,PNG,EPS,XFIG,SVG}

- InFile

  Secondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}

### Main options:

- **-algorithm**

  Drawing algorithm, chosen from \[naview,line,radiate,circular\]

- **-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**

  Look and feel for base pairs drawings, chosen from \[lw,lwalt,none,simple,rnaviz\]

- **-h**

  Displays a short description of main options and exits

- **-periodNum**

  Periodicity of base-numbering

- **-x**

  Displays a detailed description of all options

### Advanced options:

- **-annotations**

  A set of textual annotations

- **-applyBasesStyle**

  Base style application

**-autoHelices**

**-autoInteriorLoops**

**-autoTerminalLoops**

- **-auxBPs**

  Adds a list of (possibly non-canonical) base-pairs to those already defined by the main secondary structure (Ex: "(1,10);(2,11);(3,12)"). Custom BP styles c

-

  an be specified (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**

  Distance between nested base-pairs (i.e. arcs) in linear representation

**-chemProb**

- **-colorMap**

  Associates a list of numerical values (eg '0.2,0.4,0.6,0.8') with the RNA base s with respect to their natural order, and modifies the color used to fill the se bases according to current color map style.

- **-colorMapCaption**

  Sets current color map caption.

**-colorMapMax**

**-colorMapMin**

- **-colorMapStyle**

  Selects a specific color map style. It can be either one of the predefined sty les (eg 'red', 'green', 'blue', 'bw', 'heat', 'energy') or a new one (eg '0:#F FFF00;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/hide the outline of bases

**-drawColorMap**

- **-drawNC**

  Toggles on/off display of non-canonical base-pairs

- **-drawTertiary**

  Toggles on/off display of tertiary interaction, ie pseudoknots

- **-error**

  Show errors

- **-fillBases**

  Fills or leaves empty the inner portions of bases

- **-firstSequence**

  In comparison mode, sequence of first RNA

- **-firstStructure**

  In comparison mode, structure of 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 clockwi se order (default drawing is counter-clockwise). The argument is a semicolon-s eparated list of helices, each identified by a base or a base-pair (eg. "2;20- 34").

- **-gapsColor**

  Define and use custom color for gaps bases in comparison mode

- **-highlightRegion**

  Highlight a set of contiguous regions

- **-modifiable**

  Allows/prohibits modifications

- **-nsBasesColor**

  Define and use 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 RNA after initial drawing (Ex: '20' for a 20 degree counter-clockwise rotation)

- **-rows**

  Sets number of columns

- **-secondSequence**

  In comparison mode, sequence of second RNA

- **-secondStructure**

  In comparison mode, structure of 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