Abstract
Up to now, many algorithms and programs for repeat sequences detection (such as tandem repeats finder [2], REPuter [4], color coding [5], and so on) have been developed and applied to genome sequence analysis. In the present study, a visualization algorithm for detecting and analyzing the repetitive sequences in genomes is proposed. The present method is based on a dot plot between identical sequences. We call the present method Adplot (this name comes from the abbreviation of “auto dot plot”). Adplot can process any length DNA sequence at once (in practice) and requires relatively small computation resources for execution. In particular, Adplot is suitable for detecting a) repeats with a long unit length and b) tandem repeats and non-tandem relatively distant repeats (close repeats), and c) for analyzing complex structures of repetitive patterns.
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