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Deposited research article

Short segmental duplication: parsimony in growth of microbial genomes

Li-Ching Hsieh¹, Liaofu Luo⁴ and Hoong-Chien Lee^2,3

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

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

³National Center for Theoretical Sciences, Shinchu, Taiwan

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

author email corresponding author email

Genome Biology 2003, 4:P7doi:10.1186/gb-2003-4-9-p7

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

Subject areas: Methods, Microbiology and parasitology, Genome studies, Evolution

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2003/4/9/P7

Received:	1 August 2003
Posted:	4 August 2003

© 2003 BioMed Central Ltd

Abstract

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

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