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Proceedings Paper

Symmetries in the genome structure of Bacillus subtilis shown by doublet frequency maps
Author(s): Johann Michael Koehler
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Paper Abstract

A method of visualisation of sequence patterns in genomes was applied on the study of the structure of the genome of the Gram-positive bacterium Bacillus subtilis. The information stored in more or less strong noised symmetnes, strange sequence parts and other features of DNA sequences related to the evolution of genomes can be visualised by a graphical representation of doublet frequency distributions. The method gives an insight in the weak relationships between different parts ofthe genome. A very clear subdivision ofthe genome in two parts ofnearly equal size (about 2 million bp) is reflected by the distribution ofdoublet frequencies. The pattern also shows the inclusion ofthe known prophages and prophages-like structures as strips of strange sequence segments in the matrix pattern. The method is particularly suiteable for the visualisation of translational symmetries. The doublet frequency maps show clearly segments, which are doubled or multiplied in the genome. Sequence segments with a comparatively low degree ofrelations become visible beside identical sequence parts. A sequence segment of about 5,5 kb existing 9 times was found in four single, a double and a triple arrangement. Hexaplet correlationmaps andmaps ofthe correlation ofdoublet frequencies ofcoded amino acids are suitable well for the detection of symmetries in the genome of Bacillus subtilis and supply an increased contrast in case of noised duplications oflarger sequence segments. In summary, the visualisation reflects obviously the evolution ofthe genome by an hierarchy of insertions and duplications with characteristically doublet contents in a matrix of more homogenous distributed doublet frequencies.

Paper Details

Date Published: 5 June 2002
PDF: 9 pages
Proc. SPIE 4623, Functional Monitoring and Drug-Tissue Interaction, (5 June 2002); doi: 10.1117/12.491254
Show Author Affiliations
Johann Michael Koehler, Institut fuer Physikalische Hochtechnologie e.V. (Germany)

Published in SPIE Proceedings Vol. 4623:
Functional Monitoring and Drug-Tissue Interaction
Manfred D. Kessler; Gerhard J. Mueller, Editor(s)

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