DNA Repeats Detection Using a Dedicated Dot-Plot Analysis

DNA repeats are believed to play significant roles in genome evolution and diseases. Many of the methods for finding repeated sequences are part of the digital signal processing (DSP) field and most of these methods use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using DNA distances and consensus types) and a custom dot-plot analysis (using similarities to represent DNA patterns) combined with image processing techniques, to visual isolate the position of DNA patterns with different lengths. The final images that best put in evidence the presence of repeated sequences were obtained using weighted cosine cross-correlation, Jukes-Cantor distance and Motyka similarity.