A rigorous definition of Tandem Repeats (TR) is proposed, and a sensitive method is presented for TR detection in genomic data. The heart of our method lays on organizing the information provided by a pattern discovery tool, TEIRESIAS. The latter is a model-less algorithm, and thus our method inherits the feature of not relying on a predetermined model. Using this technique, we made a systematic study of the TR in the yeast S. Cerevisiae. We studied the distribution of periods and copy-numbers as well as the proportion of TR in coding vs. non-coding regions. With respect to the later, we found that for periods greater than 10, 60% of the TR lay on coding regions. We also discuss the phenomenon of nesting of TR (which occurs when a TR is contained within another TR locus). Finally we study patterns that are common to the yeast TR.
By: Gustavo Stolovitzky, Y. Gao, A. Floratos, I. Rigoutsos
Published in: RC21508 in 1999
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