varna - Assisted drawing of RNA secondary structure
java -cp . [-i InFile|-sequenceDBN XXX
-structureDBN YYY] -o OutFile [Options]
VARNA v3.9 Assisted drawing of RNA secondary structure (Command
Line version)
- OutFile
- Supported formats: {JPEG,PNG,EPS,XFIG,SVG}
- InFile
- Secondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}
- -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
- -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