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Insights into bacterial genome composition through variable target GC content profiling

Mann, Scott, Li, Jinyan and Chen, Yi-Ping Phoebe 2010, Insights into bacterial genome composition through variable target GC content profiling, Journal of computational biology, vol. 17, no. 1, pp. 79-96.

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Title Insights into bacterial genome composition through variable target GC content profiling
Author(s) Mann, Scott
Li, Jinyan
Chen, Yi-Ping Phoebe
Journal name Journal of computational biology
Volume number 17
Issue number 1
Start page 79
End page 96
Total pages 18
Publisher Mary Ann Liebert Publishers
Place of publication New York, N. Y.
Publication date 2010-01
ISSN 1066-5277
1557-8666
Keyword(s) bacteria genome nucleotide usage
Buchnera
G+C content
genome reduction
Staphylococcus
Summary This study presents a new computational method for guanine (G) and cytosine (C), or GC, content profiling based on the idea of multiple resolution sampling (MRS). The benefit of our new approach over existing techniques follows from its ability to locate significant regions without prior knowledge of the sequence, nor the features being sought. The use of MRS has provided novel insights into bacterial genome composition. Key findings include those that are related to the core composition of bacterial genomes, to the identification of large genomic islands (in Enterobacterial genomes), and to the identification of surface protein determinants in human pathogenic organisms (e.g., Staphylococcus genomes). We observed that bacterial surface binding proteins maintain abnormal GC content, potentially pointing to a viral origin. This study has demonstrated that GC content holds a high informational worth and hints at many underlying evolutionary processes. For online Supplementary Material, see www.liebertonline.com.
Language eng
Field of Research 080301 Bioinformatics Software
Socio Economic Objective 890299 Computer Software and Services not elsewhere classified
HERDC Research category C1 Refereed article in a scholarly journal
HERDC collection year 2010
Copyright notice ©2010, Mary Ann Liebert Publishers
Persistent URL http://hdl.handle.net/10536/DRO/DU:30034414

Document type: Journal Article
Collections: School of Information Technology
Open Access Collection
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