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Strong GC and AT Skew Correlation in Chicken Genome

  • Xuegong Deng
  • Xuemei Deng
  • Ilkka Havukkala
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4774)

Abstract

Chicken genome AT and GC skews for individual chromosomes were visualized simultaneously using a novel method of 2-dimensional color-coded pixel matrix. The visualizations were compared to those of human, mouse and possum genomes. A strikingly strong correlation of AT skew and GC from small to large scale in chicken genome was found, compared to the other vertebrates. Some local skew correlations were also found for the other vertebrates, but only in small genomic scale. Quantitative measures of correlation were developed, and confirmed the special characteristic of chicken chromosomes. Possible explanations for uniqueness of birds in this respect are discussed. The phylogenetic distribution and evolutionary pressures responsible for this previously unreported skew correlation warrant further study.

Keywords

AT/GC skew skew correlation chicken genome chromosome visualization 2D 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Xuegong Deng
    • 1
  • Xuemei Deng
    • 2
  • Ilkka Havukkala
    • 3
  1. 1.Northeastern university, College of Science, ShenyangChina
  2. 2.Department of Animal Genetics and Breeding & National Key Lab, China Agricultural University, Beijing 100094China
  3. 3.Auckland University of Technology, Knowledge Engineering and Discovery Research Institute, AucklandNew Zealand

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