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Short segmental duplication: parsimony in growth of microbial genomes

Li-Ching Hsieh1, Liaofu Luo4 and Hoong-Chien Lee23*

Author Affiliations

1 Department of Physics, National Central University, Chungli, Taiwan 320

2 Department of Life Sciences, National Central University, Chungli, Taiwan 320

3 National Center for Theoretical Sciences, Shinchu, Taiwan

4 Department of Physics, Inner Mongolia University, Hohot, China

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Genome Biology 2003, 4:P7  doi:10.1186/gb-2003-4-9-p7

This was the first version of this article to be made available publicly.

The electronic version of this article is the complete one and can be found online at:

Received:1 August 2003
Published:4 August 2003

© 2003 BioMed Central Ltd


We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long (2 to 10-mers) in microbial complete genomes with corresponding distributions obtained from random sequences and find that the genomic distributions are uniformly many times wider in a universal manner, that is, the same for all microbial complete genomes. The difference increases with decreasing word length, with the genomic spectral width about 40 times wider for 2-mers. We show that the observed genomic properties are characteristic of sequences generated in a simple growth model, where a very short initial random sequence (less than 1 kb) grows mainly by maximally stochastic duplication of short segments (of about 25 b). We discuss a number issues related to the findings and the model, including the proposition that life began in an RNA world before the birth of proteins.

Deposited research article