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

varna 3-93+ds                                       July 2024                                           VARNA(1)