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Bioinformatics. 2015 Oct 15;31(20):3348-9. doi: 10.1093/bioinformatics/btv376. Epub 2015 Jun 20.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

Author information

1
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 and.
2
Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.

Abstract

MOTIVATION:

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations.

RESULTS:

GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general.

AVAILABILITY AND IMPLEMENTATION:

GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/.

CONTACT:

brinkman@sfu.ca.

PMID:
26093150
PMCID:
PMC4595901
DOI:
10.1093/bioinformatics/btv376
[Indexed for MEDLINE]
Free PMC Article

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