RiboSketch

Bond editing, E. Coli 5S rRNA with SHAPE data coloring
Hexameric Ring with arms
Dengue Virus
Hexameric Ring, dynamic formation
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Use RiboSketch Online

Bioinformatics Publication
If you use RiboSketch in your scientific work, we would greatly appreciate a citation to our publication.

What is RiboSketch?

  • RiboSketch is a drawing program for the production of RNA and DNA secondary structure images.
  • The user provides an input file (.ct, .bpseq, .dbn, or the save file type .rs) containing the sequence and base-pairing of the strand(s).

Features

  • Works with multiple strands, non-canonical interactions, hybrid RNA-DNA base-pairing, pseudoknots, and interstrand interactions
  • Creates automatic layouts and circle diagrams
  • Dynamic simulation mode
  • Interactive editing is enabled through precise commands
  • The user may save the state of the program and load previous save-states
  • Actions may be undone and redone

Using the Program

  • Load a secondary structure file (you can add additional bonds and non-canonicals once in the program)
  • Default start state is the “Radial Layout”.
  • Mouse over the top of the screen to access the MENU and to view COMMANDS.

Mouse Commands

  • Click on (or drag a selection box over) bases to select them. Hold shift to multi-select or toggle the selection of bases.
  • Drag selected nucleotides to move them.
  • To select individual nucleotides, hold ALT/OPTION and click.
  • To select one half of a helix, you can either:
    • Select the helix, then shift click on the side you don't want to unselect it.
    • Click and drag a selection box over one side of the helix.
  • ROTATION: “m” rotates clockwise about the mouse cursor, “n” counterclockwise. Hold shift to rotate with a smaller angle.

Menu Features

Sliders

  • Base Size: Size of nucleotides
  • Bond Length: Distance between base-paired nucleotides
  • Chain Length: Effective only during simulation mode, controls distance between adjacent nucleotides
  • Color Scheme: “Pastel”, “White”, "Light", “Bright”, “Grey", and special ones:
    • Base Type: Each nucleotide type gets its own color
    • Rainbow: Each individual base gets its own color
    • Structure: Paired bases: Yellow, Unpaired: Blue
    • Custom: User must input number values corresponding to each base

Buttons

  • Save: Writes state of program into a text file (.rs), which can be loaded into RiboSketch.
  • Load File: Read a new secondary structure file into the program.
  • Load Bonds: Add new bonds from a text file of comma-separated entries with format: “firstID secondID bondType”
    • Example: 3 20 cWW, 4 19 tHS, 6 30 cSS
  • Load Colors: Color nucleotides based on a space-separated list of numbers (probing data) from a text file.
  • Radial Layout: Position nucleotides with the NAView algorithm, expanded to accommodate multiple strands and pseudoknots.
  • Circle Layout: Nucleotides are positioned in a circle with base pairs drawn as chords.
  • Simulation Mode: Apply forces.
  • Sim. Selected Mode: Only apply forces to selected nucleotides.
  • Rigid Helices: Enforce right angles for helices.
  • Rigid Loops: Circularize loops and straighten stems.
  • Rigid Hairpins: Circularize hairpin loops. Only has effect when Rigid Loops is OFF.
  • Zoom Reset: Return zoom to default.
  • Outlines: Toggle drawing circles around nucleotides.
  • Labels: Display numbering for every tenth nucleotide.
  • PNG Screenshot: Saves a screen image to the folder of the input file.
  • SVG Screenshot: Saves an SVG file of the screen to the folder of the input file.

Keyboard Commands

Editing

  • ROTATION: “m” rotates clockwise about the mouse cursor; “n” counterclockwise. Hold shift to rotate with a smaller angle.
  • "z": UNDO. Shift-Z to REDO.
  • "s": Turn on or off SIMULATION (forces)
  • "S": Toggle the SIMULATION MODE to apply forces to selected nucleotides only or all nucleotides.
  • “f”: FLIP the halves of a selected helix.
  • “x” or “y”: Flips the selected bases over the X or Y-axis.
  • "r": RELAX FORCES for selected nucleotides. Effective only in Simulation mode.

Display

  • + / - : Zooms the screen in or out
  • 0 : Resets the view scale
  • Arrows : When no nucletodies are selected, the arrow keys translate the window view.
  • 1 / 2 : Brings the selected bases to the front or back, akin to Powerpoint
  • b / B : Base SIZE +/- (Same as slider)
  • o : Toggle OUTLINE
  • i : Toggle LETTERS
  • l : Toggle LABELS (Same as button)
  • k : View base number in secondary file
  • v : Toggle ANNOTATIONS (5' and 3', strand number)
  • c : Changes the color scheme of the nucleotides
  • p : Saves a PNG SCREENSHOT (Same as the button)

Adding and Deleting Bonds

  • Adding: Hold Spacebar, click first base, click second base.
  • Non-Canonical: Click "Load Bonds" button to add bonds of a specified type through text input (Ex: 3 25 cWW, 8 12 tHS)
  • Deleting: Hold "d", click a base to delete its bonds.

The "RS" Data Format

The state of the program can be saved using the "RS" format (RS stands for RiboSketch), a special case of the Java Properties format: In other words, a text file in which keys and values are separated by an equals ("=") character. Comment lines (preceded by the "#" character) are allowed. Recognized keys are:
  1. sequences: semicolon-separated list of RNA or DNA sequence strings which are in upper or lower case respectively
  2. starts: comma-separated list of zero-based indices of the first residue of each sequence
  3. positions: semicolon-separated string of x,y,z positions of each residue. In the current version the z-values are set to zero.
  4. radius: the radius of the residues in pixel units
  5. backbone_distance: target distance of two residues that are adjacent in sequence
  6. basepair_distance: target distance of two base paired residues
  7. color_scheme: an integer that stands for the color mode
  8. outline: true/false indicating whether the residues are drawn with a black circle
  9. movement: true/false indicating whether the simulation mode is on
  10. labels: true/false indicating whether the residue labels are shown or not
  11. rigid_helices: true/false indicating whether rigidifying helices is activated or not
  12. rigid_loops: true/false indicating whether rigidifying loops is activated or not
  13. rigid_hairpins: true/false indicating whether rigidifying hairpins is activated or not
  14. relax_ids: comma-separated list of residues whose basepairs are not affected by forces
  15. display_order: residues are displayed in this order. This is useful in order to achieve foreground/background effects
  16. pair_table: residue partners for each base pair (-1 for unpaired bases). Similar to base pair column in a CT format file.
  17. non_canonicals: extra information about non-canonical base pairs
  18. base_colors: assignable colors for each base (comma-separated RGB values between 0 and 1)

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