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DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes

Title:

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes

Neugebauer, Tomasz ORCID: https://orcid.org/0000-0002-9743-5910, Bordeleau, Eric, Burrus, Vincent and Brzezinski, Ryszard (2015) DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes. PLOS ONE, 10 (12). e0143615. ISSN 1932-6203

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Official URL: http://dx.doi.org/10.1371/journal.pone.0143615

Abstract

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

Divisions:Concordia University > Library
Item Type:Article
Refereed:Yes
Authors:Neugebauer, Tomasz and Bordeleau, Eric and Burrus, Vincent and Brzezinski, Ryszard
Journal or Publication:PLOS ONE
Date:2015
Funders:
  • Concordia Open Access Author Fund
Digital Object Identifier (DOI):10.1371/journal.pone.0143615
Keywords:Data visualization, Chromosomes, Nucleotide sequencing, Bacterial genomics, Genome analysis, Ribosomal RNA, DNA sequence analysis
ID Code:980761
Deposited By: TOMASZ NEUGEBAUER
Deposited On:21 Dec 2015 18:03
Last Modified:18 Jan 2018 17:51
Related URLs:

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