Table of Contents
ISRN Bioinformatics
Volume 2013 (2013), Article ID 725434, 6 pages
http://dx.doi.org/10.1155/2013/725434
Research Article

IsoPlotter+: A Tool for Studying the Compositional Architecture of Genomes

1Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
2Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA

Received 5 March 2013; Accepted 1 April 2013

Academic Editors: A. Bolshoy, B. Haubold, D. A. McClellan, A. Pulvirenti, and K. Yura

Copyright © 2013 Eran Elhaik and Dan Graur. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Eukaryotic genomes, particularly animal genomes, have a complex, nonuniform, and nonrandom internal compositional organization. The compositional organization of animal genomes can be described as a mosaic of discrete genomic regions, called “compositional domains,” each with a distinct GC content that significantly differs from those of its upstream and downstream neighboring domains. A typical animal genome consists of a mixture of compositionally homogeneous and nonhomogeneous domains of varying lengths and nucleotide compositions that are interspersed with one another. We have devised IsoPlotter, an unbiased segmentation algorithm for inferring the compositional organization of genomes. IsoPlotter has become an indispensable tool for describing genomic composition and has been used in the analysis of more than a dozen genomes. Applications include describing new genomes, correlating domain composition with gene composition and their density, studying the evolution of genomes, testing phylogenomic hypotheses, and detect regions of potential interbreeding between human and extinct hominines. To extend the use of IsoPlotter, we designed a completely automated pipeline, called IsoPlotter+ to carry out all segmentation analyses, including graphical display, and built a repository for compositional domain maps of all fully sequenced vertebrate and invertebrate genomes. The IsoPlotter+ pipeline and repository offer a comprehensive solution to the study of genome compositional architecture. Here, we demonstrate IsoPlotter+ by applying it to human and insect genomes. The computational tools and data repository are available online.