VARNA

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, choosen 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, choosen from [lw,lwalt,none,simple,rnaviz]

-h

Displays a short description of main options and exits

-periodNum

Periodicity of base-numbering

-x

Displays a detailled 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