Table of Contents
ISRN Bioinformatics
Volume 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.

Linked References

  1. D. Graur and W.-H. Li, Fundamentals of Molecular Evolution, Sinauer Associates, Sunderland, Mass, USA, 2000.
  2. C. G. Elsik, R. L. Tellam, K. C. Worley et al., “The genome sequence of taurine cattle: a window to ruminant biology and evolution,” Science, vol. 324, no. 5926, pp. 522–528, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. E. Elhaik, D. Graur, K. Josić, and G. Landan, “Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm,” Nucleic Acids Research, vol. 38, no. 15, article 158, 2010. View at Google Scholar · View at Scopus
  4. N. Cohen, T. Dagan, L. Stone, and D. Graur, “GC composition of the human genome: in search of isochores,” Molecular Biology and Evolution, vol. 22, no. 5, pp. 1260–1272, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. G. Bernardi, B. Olofsson, and J. Filipski, “The mosaic genome of warm-blooded vertebrates,” Science, vol. 228, no. 4702, pp. 953–958, 1985. View at Google Scholar · View at Scopus
  6. E. M. S. Belle, N. Smith, and A. Eyre-Walker, “Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis,” Journal of Molecular Evolution, vol. 55, no. 3, pp. 356–363, 2002. View at Publisher · View at Google Scholar · View at Scopus
  7. L. Duret and N. Galtier, “Biased gene conversion and the evolution of mammalian genomic landscapes,” Annual Review of Genomics and Human Genetics, vol. 10, pp. 285–311, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. W.-H. Li, “On parameters of the human genome,” Journal of Theoretical Biology, vol. 288, pp. 92–104, 2011. View at Google Scholar
  9. A. Eyre-Walker and L. D. Hurst, “The evolution of isochores,” Nature Reviews Genetics, vol. 2, no. 7, pp. 549–555, 2001. View at Publisher · View at Google Scholar · View at Scopus
  10. E. Elhaik, D. Graur, and K. Josić, “Comparative testing of DNA segmentation algorithms using benchmark simulations,” Molecular Biology and Evolution, vol. 27, no. 5, pp. 1015–1024, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. C. R. Smith, C. D. Smith, H. M. Robertson et al., “Draft genome of the red harvester ant Pogonomyrmex barbatus,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 14, pp. 5667–5672, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. C. D. Smith, A. Zimin, C. Holt et al., “Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile),” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 14, pp. 5673–5678, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. G. Suen, C. Teiling, L. Li et al., “The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle,” PLoS Genetics, vol. 7, no. 2, Article ID e1002007, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. E. Sodergren, G. M. Weinstock, E. H. Davidson, R. A. Cameron, R. A. Gibbs et al., “Insights into social insects from the genome of the honeybee Apis mellifera,” Nature, vol. 443, pp. 931–949, 2006. View at Google Scholar
  15. E. F. Kirkness, B. J. Haas, W. Sun, H. R. Braig, M. A. Perotti et al., “Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, pp. 12168–12173, 2010. View at Google Scholar
  16. J. H. Werren, S. Richards, C. A. Desjardins, O. Niehuis, J. Gadau et al., “Functional and evolutionary insights from the genomes of three parasitoid Nasonia species,” Science, vol. 327, pp. 343–348, 2010. View at Google Scholar
  17. E. Sodergren, G. M. Weinstock, E. H. Davidson et al., “The genome of the sea urchin Strongylocentrotus purpuratus,” Science, vol. 314, no. 5801, pp. 941–952, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. S. Richards, R. A. Gibbs, G. M. Weinstock et al., “The genome of the model beetle and pest Tribolium castaneum,” Nature, vol. 452, no. 7190, pp. 949–955, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. D. F. Simola, L. Wissler, G. Donahue, R. M. Waterhouse, M. Helmkampf et al., “The (r)evolution of social insect genomes,” Proceedings of the National Academy of Sciences.
  20. E. Elhaik, G. Landan, and D. Graur, “Can GC content at third-codon positions be used as a proxy for isochore composition?” Molecular Biology and Evolution, vol. 26, no. 8, pp. 1829–1833, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. E. Elhaik and T. V. Tatarinova, “GC3 biology in eukaryotes and prokaryotes,” in DNA Methylation—From Genomics To Technology, T. Tatarinova and O. Kerton, Eds., pp. 55–68, 2012. View at Google Scholar
  22. T. V. Tatarinova, N. N. Alexandrov, J. B. Bouck, and K. A. Feldmann, “GC3 biology in corn, rice, sorghum and other grasses,” BMC Genomics, vol. 11, no. 1, article 308, 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. E. Elhaik, E. Greenspan, E. S. Staats, T. Krahn, C. Tyler-Smith et al., “The GenoChip: a new tool for genetic anthropology,” Genome Biology and Evolution.
  24. M. Costantini, O. Clay, F. Auletta, and G. Bernardi, “An isochore map of human chromosomes,” Genome Research, vol. 16, no. 4, pp. 536–541, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. J. L. Oliver, P. Carpena, M. Hackenberg, and P. Bernaola-Galván, “IsoFinder: computational prediction of isochores in genome sequences,” Nucleic Acids Research, vol. 32, pp. W287–W292, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. D. Mouchiroud, C. Gautier, and G. Bernardi, “The compositional distribution of coding sequences and DNA molecules in humans and murids,” Journal of Molecular Evolution, vol. 27, no. 4, pp. 311–320, 1988. View at Google Scholar · View at Scopus
  27. A. McLysaght, D. Huson, L. Carmel, I. B. Rogozin, Y. I. Wolf, and E. V. Koonin, “An expectation-maximization algorithm for analysis of evolution of exon-intron structure of eukaryotic genes,” Comparative Genomics, vol. 3678, pp. 35–46, 2005. View at Publisher · View at Google Scholar · View at Scopus