lunar (1) varna.1.gz
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