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.
Highlights
Information visualization can amplify cognition by storing massive amounts of information in quickly accessible forms and using visual representations to enhance the detection of patterns [1].Visualization of genomic data augments reasoning and analysis by facilitating the PLOS ONE | DOI:10.1371/journal.pone.0143615 December 4, 2015DNA Data Visualization Software for Entire Genomes the Natural Sciences and Engineering Council of Canada [326810 and 412288] to VB and Discovery Grant 2014-05177 to RB
The visualization method presented in this work allows immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins, often not identified by other methods
We present a novel method for generating visual representations of nucleotide sequences
Summary
Information visualization can amplify cognition by storing massive amounts of information in quickly accessible forms and using visual representations to enhance the detection of patterns [1].Visualization of genomic data augments reasoning and analysis by facilitating the PLOS ONE | DOI:10.1371/journal.pone.0143615 December 4, 2015DNA Data Visualization Software for Entire Genomes the Natural Sciences and Engineering Council of Canada [326810 and 412288] to VB and Discovery Grant 2014-05177 to RB. Information visualization can amplify cognition by storing massive amounts of information in quickly accessible forms and using visual representations to enhance the detection of patterns [1].Visualization of genomic data augments reasoning and analysis by facilitating the PLOS ONE | DOI:10.1371/journal.pone.0143615. DNA Data Visualization Software for Entire Genomes the Natural Sciences and Engineering Council of Canada [326810 and 412288] to VB and Discovery Grant 2014-05177 to RB. VB holds a Canada Research Chair in Bacterial Molecular Genetics. EB is the recipient of a Cystic Fibrosis Canada-Kin Canada Fellowship and a postdoctoral fellowship from Le Fonds de Recherche du Québec – Santé (FRQS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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