In many situations, the user interaction is superfluous and the desired goal is to simply display a secondary structure on a web page. This is a common scenario in, for example, servers that predict a secondary structure. The output, a dot-bracket string can simply be added to a FornaContainer object to display.

Trivial Example

Below is an example of a simple web page which uses a FornaContainer to show a simple RNA molecule:

blah blah

The code for creating this web page is rather straightforward. After importing some necessary javascript files, we create a container using new FornaContainer("#rna_ss", {'applyForce': false}), passing in #rna_ss as the id of the div which will hold the container and then populate it with a structure and sequence using container.addRNA:

<!DOCTYPE html>
<meta charset="utf-8">

This is an RNA container.
<div id='rna_ss'> </div>
This after the RNA container.

    <link rel='stylesheet' type='text/css' href='styles/fornac.css' />
    <script type='text/javascript' src='scripts/fornac.js'></script>
    <script type='text/javascript'>
        var container = new FornaContainer("#rna_ss", {'applyForce': false});

        var options = {'structure': '((..((....)).(((....))).))',
                        'sequence': 'CGCUUCAUAUAAUCCUAAUGACCUAU'
        };

        container.addRNA(options.structure, options);
    </script>

Cofolded sequences

Display two cofolded sequences using the format of RNAcofold:

Cofolded sequences

    var container = new fornac.FornaContainer("#cofold_ss",
            {'applyForce': false, 'allowPanningAndZooming': true, 'initialSize':[500,300]});
                                                     
    var options = {'structure': '..((((...))))...((...((...((..&............))...))...))..',
        'sequence': 'ACGAUCAGAGAUCAGAGCAUACGACAGCAG&ACGAAAAAAAGAGCAUACGACAGCAG'
    };                                                                                     
    container.addRNA(options.structure, options);
    container.setSize();

Options

The FornaContainer supports a number of options to allow users to customize how the RNA will be presented.

applyForce

Indicate whether the force-directed layout will be applied to the displayed molecule. Enabling this option allows users to change the layout of the molecule by selecting and dragging the individual nucleotide nodes

allowPanningAndZooming [default=true]

Allow users to zoom in and pan the display. If this is enabled then pressing the 'c' key on the keyboard will center the view.

circularizeExternal [default=true]

This only makes sense in connection with the applyForce argument. If it's true, the external loops will be arranged in a nice circle. If false, they will be allowed to flop around as the force layout dictates:

labelInterval [default=10]

Change how often nucleotide numbers are labelled with their number.

Implementation

Each RNA molecule is represented as a JSON file which encodes all of the information necessary to display it. The example shows a trivial and slightly modified example. nodeType can be either nucleotide or label or middle, the latter of which is used only as a placeholder for maintaining an aesthetically pleasing layout.

The links can be any of basepair (representing a basepair between two nucleotides), backbone (backbone bond between adjacent nodes), pseudoknot (pseudoknot, extracted from the specified structure using maximum matching algorithm), extra (extra links specified by the user), label_link (links between nucleotides and their nucleotide number labels), fake (invisible links for maintaining the layout), and fake_fake (invisible links for maintaining the layout).

This structure is initially created in rnagraph.js starting from a sequence and dotbracket string.

{
  "nodes": 
    [ {
      "name": "A",
      "num": 1,
      "radius": 5,
      "rna": null,
      "nodeType": "nucleotide",
      "structName": "empty",
      "elemType": "e",
      "uid": "44edb966-aca9-4058-a6bc-784a34959329",
      "linked": false,
      "prevNode": null,
      "nextNode": null,
      "x": 100,
      "px": 100,
      "y": 100,
      "py": 100
    },
    ...
    ],
  "links": 
    [ {
      "source": null,
      "target": null,
      "linkType": "basepair",
      "value": 1,
      "uid": "6664a569-5af1-4d86-8ada-d1c00da72a899f87a224-52a0-4ede-a29c-04fddc09e4c4"
      },
      ...
    ]
}

Development

First:

npm install
bower install

To debug:

gulp serve

To build:

gulp build

The output will be placed in the dist directory. To use fornac in a web page, simply include dist/scripts/fornac.js in your web page.

FAQs

What is fornac?

Is fornac well maintained?

Package last updated on 23 Feb 2016

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Install

fornac

FornaContainer

Trivial Example

Cofolded sequences

Options

applyForce

allowPanningAndZooming [default=true]

circularizeExternal [default=true]

labelInterval [default=10]

Implementation

Development

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