CAGO: A Software Tool for Dynamic Visual Comparison and Correlation Measurement of Genome Organization

Yi-Feng Chang,Chuan-Hsiung Chang,Arkady B Khodursky

doi:10.1371/journal.pone.0027080

Yi-Feng Chang, Chuan-Hsiung Chang + Show 1 more

Open Access

https://doi.org/10.1371/journal.pone.0027080

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Journal: PloS one	Publication Date: Nov 17, 2011
Citations: 17	License type: CC BY 4.0

Affiliation: National Yang Ming Chiao Tung University

Abstract

CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG) format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

Highlights

Genome atlas plotters are usually designed to plot genomic features and genomic properties of a genome as chromosome tracks in a static picture (Table S1)
We developed CAGO (Comparative Analysis of Genome Organization) to address these shortcomings by integrating dynamic exploratory functions into a genome atlas tool and implementing signal analysis functions to analyze genomic properties
In our web-based CAGO, 222 (149 for eukaryotic sequences) genomic features and genomic properties (See Table S2) are applied to the sequences downloaded from the NCBI ftp site [21]

Summary

Introduction

Genome atlas plotters ( known as genome diagram plotters or chromosome atlas plotters) are usually designed to plot genomic features (positional annotations) and genomic properties (numerical values) of a genome as chromosome tracks in a static picture (Table S1). A static genome atlas does not provide the functions of dynamic exploratory and signal analysis for genomic properties. We developed CAGO (Comparative Analysis of Genome Organization) to address these shortcomings by integrating dynamic exploratory functions into a genome atlas tool and implementing signal analysis functions to analyze genomic properties. The dynamic exploratory functions are not like the navigating and zooming functions of conventional genome browsers, but are designed to interactively manipulate each individual track of a genome atlas by modifying its image attributes. Users can change the color opacity of tracks and reposition a track onto other tracks with the interactive functions, and compare similarities or differences between different genomic features or genomic properties by visual comparison. Users can identify inconspicuous periodic patterns from a genomic property by autocorrelation [2] and calculate correlations between different genomic properties across multiple organisms by cross-correlation analysis [3]

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