This article has not been peer reviewed.
Deposited research articleShort segmental duplication: parsimony in growth of microbial genomes
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* Corresponding author: Hoong-Chien Lee hclee@phy.ncu.edu.tw
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
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.
Published: 4 August 2003Abstract
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.