https://github.com/cmdcolin/frameviewer

A JBrowse plugin for viewing which reading frame a coding region is in
https://github.com/cmdcolin/frameviewer

Last synced: 4 days ago
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A JBrowse plugin for viewing which reading frame a coding region is in

• Host: GitHub
• URL: https://github.com/cmdcolin/frameviewer
• Owner: cmdcolin
• Created: 2017-02-07T04:40:37.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2018-02-19T01:13:42.000Z (over 6 years ago)
• Last Synced: 2024-04-15T02:14:34.719Z (7 months ago)
• Language: JavaScript
• Size: 10.5 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog.md

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README

        
# frameviewer

A JBrowse plugin for viewing protein/DNA sequences of coding sequences of genes.

## Screenshot

![](img/1.png)

Figure 1. Shows protein translations and reading frames for a gene

## Configuration

* style.frameHeight - the height of the feature that contains the frames. Default: 50px

* showProtein - show the protein sequence of coding regions on the glyph. Default: false

* showDNA - show the DNA of coding regions on the glyph. Default: false

## Example

    {

     "label" : "dictyBase frames",

     "urlTemplate" : "tracks/dictyBase/{refseq}/trackData.json",

     "storeClass" : "JBrowse/Store/SeqFeature/NCList",

     "type" : "FrameViewer/View/Track/Frames",

     "showProtein": true

    }

The test/data/ directory contains a sample config also.

## Installation

Download to plugins/FrameViewer and add

    "plugins": ["FrameViewer"]

to jbrowse_conf.json or trackList.json. See JBrowse FAQ on installing plugins for more details

## Feedback

Please let me know if you have feedback or know of crazy biology corner cases that need covering!

Note: code currently contains glitches that make this not production ready