A web server for interactive and zoomable Chaos Game Representation images

Kazuharu Arakawa,Masaru Tomita,Kazuki Oshita

doi:10.1186/1751-0473-4-6

Kazuharu Arakawa, Masaru Tomita + Show 1 more

Open Access

https://doi.org/10.1186/1751-0473-4-6

Copy DOI

Abstract

Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of characteristic sequence motifs. However, in order to fully utilize the scale-independent properties of CGR, it should be accessible through scale-independent user interface instead of static images. Here we describe a web server and Perl library for generating zoomable CGR images utilizing Google Maps API, which is also easily searchable for specific motifs. The web server is freely accessible at , and the Perl library as well as the source code is distributed with the G-language Genome Analysis Environment under GNU General Public License.

Highlights

Genomic sequences exhibit characteristic nucleotide compositional bias, especially in the relative abundances of short oligonucleotides
K-mer table To generate k-mer table, a square is repeatedly subdivided into four squares, while retaining the quadrant representation of four nucleotides, Each box representing certain k-mer produced by our software shows the sequence and the count of k-mer (Figure 2)
Zoomable User Interface (ZUI) allow multi-scale observation of large Chaos Game Representation (CGR) image at varying magnification levels, which is suited to the scale-independent nature of CGR

Summary

Introduction

Genomic sequences exhibit characteristic nucleotide compositional bias, especially in the relative abundances of short oligonucleotides. Here we describe a web server for generating interactive and zoomable CGR images, using Google Maps API [13] and Web 2.0 technologies [14]. Chaos Game Representation In order to generate CGR for a given nucleotide sequence, a rectangular coordinate system is defined to be confined by four vertices representing the four nucleotides: A (-1, 1), C (-1, -1), G (1, 1), and T (1, -1).

Results

Conclusion