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Title: Doublet frequency maps of DNA sequences: A tool for quantitative visualization
of segment homologies
P83
Köhler, Michael (1); Wölfl, Stefan (2)

stefan.woelfl@med.uni-jena.de
(1) Department of Biotechnical Microsystems, Technische Universität Ilmenau, (2) AG Molekularbiologie Klinikum der Friedrich-Schiller-Universität Jena

The information stored in more or less strong noised symmetries, strange sequence parts and other features of DNA sequences related to the evolution of genomes can be taken very quickly from the graphical representation of doublet frequency distributions. Insertion as well as tandem duplications or multiplications are presented by vertical or tilted contrast strips in the maps. The method gives an insight in both strong and weak relationships between different sequences or whole chromosomes. Highly homolog single duplications can be visualized as well as less-related sequence parts, or multiple duplications and complex duplication patterns. As an example, differences in the frequency of doublet distributions in yeast chromosomes and sequence segments were analyzed and graphical maps generated that visualize intra- and inter-chromosomal relations. The maps visualize translational symmetries as well as symmetries with strong superposed mutational noise of sequence segments of lengths between 15 bp and more than 13 kb, that means over three orders of magnitude. They also give a visualization of complex sequence translocation patterns, which suggest an echo of the relative chronology of duplication and insertion events during the genome evolution.
[1] Koehler J. M. (1998) Evolution in Hierarchien. Jahrbuch Selbstorganisation 8, 171-183.
[2] Köhler, J. M.; Weller, K.; R. Recknagel (1993) Verwandtschaftsbeziehungen in E. Coli Promotorsequenzen, dargestellt durch Dubletthäufigkeiten 1. Fachtagung Informatik in den Biowissenschaften (Bonn Februar 1993), Informatik aktuell (Springer 1993), 101.