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J Biomol Struct Dyn. 2007 Oct;25(2):127-33.

The distribution patterns of bases of protein-coding genes, non-coding ORFs, and intergenic sequences in pseudomonas aeruginosa PA01 genome and its implications.

Author information

1
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. fbguo@uestc.edu.cn

Abstract

The distribution patterns of bases of DNA fragments in different regions in P. aeruginosa genome are analyzed in this paper. It's shown that 5565 protein-coding genes, 17315 non-coding ORFs, and 1104 intergenic sequences are located into seven clusters based on their base frequencies. Almost all the protein-coding genes are contained in one of the seven clusters. The significant difference of base frequencies among three codon positions in high GC genome, which arouse the division between the distribution patterns of bases of six reading frames of protein-coding genes, is responsible for the appearance of the clustering phenomenon. In the light of the clustering phenomenon, the author supposes that the anitisense strand ORFs, particularly those corresponding to Frame 2' and Frame 3', may not code for proteins in P. aeruginosa genome.

PMID:
17718591
DOI:
10.1080/07391102.2007.10507161
[Indexed for MEDLINE]

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