A rapid method of whole genome visualisation illustrating features in both coding and non-coding regions

摘要

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 spectraover 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 Leishma-nia major.