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

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.

• Type: Conference
• Year: 2004
• Where: APBC
• Authors: Ross Hall, Linda Stern
• Keywords: APBC 2004, APBC 2007, Fourier Analysis, Fourier Spectra, Gene Coding Regions