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Genome Biology

, 5:P7 | Cite as

Universality in large-scale structure of complete genomes

  • Li-Ching Hsieh
  • Ta-Yuan Chen
  • Chang-Heng Chang
  • Wen-Lang Fan
  • Hoong-Chien Lee
Deposited research article

Abstract

The abundance of duplications in genomes in the form of paralogs, pseudogenes and a variety of repeats suggests that genomes may have used duplications as one mode for their growth. However a systematic knowledge on all possible duplications in whole genomes is still lacking. This paper reports the results of a detailed study of occurrence frequencies of short oligonucleotides in all extant complete genomes. We found a systematic pattern of repeats of short oligonucleotides that places all the complete genomes except Plasmodium in a single universality class expressed by an extremely simple formula. Our analysis of the data combined with computer simulation of genome growth models suggest a simple coarse-grain representation of genome growth: the ancestors of the genomes began to grow when they were no greater than 300 b in length via a mechanism whose main components were neutral stochastic segmental replicative translocations and random small mutations.

Keywords

Plasmodium Complete Genome Spectral Width Universality Class Neutral Theory 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Copyright information

© BioMed Central Ltd 2004

Authors and Affiliations

  • Li-Ching Hsieh
    • 1
    • 2
  • Ta-Yuan Chen
    • 1
  • Chang-Heng Chang
    • 1
  • Wen-Lang Fan
    • 1
  • Hoong-Chien Lee
    • 1
    • 2
    • 3
  1. 1.Department of PhysicsNational Central UniversityChungli
  2. 2.Department of Life SciencesNational Central UniversityChungliTaiwan
  3. 3.Center for Complex SystemsNational Central UniversityChungliTaiwan

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