Application of fractal representation of genetic texts for recognition of genome functional and coding regions

By applying fractal representation of nucleotide sequences for plotting a set of functionally similar sequences, a new approach for classification of nucleic sequences was suggested and some measures of sequence similarity were introduced. Many examples of good separation of sequences belonging to different gene families were shown. The method does not require alignment procedure both for generating a recognition matrix of learning set and for searching homologous regions. The computer time does not depend on the length of the searching sequence and the fractal images of sequence sets can be compared easily by computer procedures as well as visually. The latter is especially convenient for representing the density of fractal mask as a third coordinate of the image. The method is successfully applied both for searching genes (globins, histories, etc.) and different kind of repetitive DNA sequences (Alu, LTR, etc.). The FRS approach is used also for revealing the gene structure in uncharacterized sequences. The fractal images for exons, introns, 5{prime}- and 3{prime}-region have significantly different patterns which permit one to find preliminary localizations of these gene regions.