ChaosGame generates the CGR of a given sequence for a certain value of k (word length). CGR graphically highlights differences in the frequencies of DNA words. To facilitate visualization, the gray levels in the image generated can be normalized in three different ways: 1) “not”: i. e. not normalized, the image will be generated in such a way that the intensity of gray of a pixel will be directly proportional to the frequency of a oligonucleotide in the sequence; 2) “auto”: the intensity of a pixel is referred to the average for all pixels (= no. of words / number of dots in the image) in such a way that pixels to which correspond frequencies above the average will have gray tones lighter than the mean gray value (intensity = 128) and the ones with frequencies below that average, darker colors; and, 3) “percentage”, ranging from 1 to 5%, in which the chosen percentage of points with top frequencies appear with the maximum value of intensity (white = 255) while the frequencies of the others are linearly normalized to fit in the rest of the gray scale (i. e. from 0 to 254). This last type of normalization is particularly useful when all the frequencies are very low (e. g. high k values). Once the gray image (pgm format) has been obtained, the user may directly visualized it or, alternatively, it may convert it into a color image using three different transformations of gray tones into pseudocolors. These color files are generated in .ppm (Portable Pixel Map) format and can also be visualized with the IrfanView program.
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