A Rapid Method of Whole Genome Visualisation Illustrating Features in Both Coding and Non-coding Regions

Hall, R. and Stern, L.

    The application of Fourier analysis to a genome can be used as an indicator of gene coding regions. We have developed a visualisation of the Fourier spectra that allows convenient whole chromosome scanning for genes and other features. The method's rapid operation suits its application as a first pass analysis. Fourier analysis indicates a strong periodicity of 3 in coding regions of several different organisms and is independent of the orientation of the gene. A bitmap display of the Fourier spectra over a sliding window gives rapid visualisation and localisation of coding regions in the chromosomes of a number of different organisms. Non-coding features such as regions of repetitive DNA, are visualised at the same time. The method works particularly well on organisms with a skewed base composition such as the malaria parasite Plasmodium falciparum and the protozoan Leishmania major.
Cite as: Hall, R. and Stern, L. (2004). A Rapid Method of Whole Genome Visualisation Illustrating Features in Both Coding and Non-coding Regions. In Proc. Second Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand. CRPIT, 29. Chen, Y.-P. P., Ed. ACS. 285-290.
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