Analysis of Tandem Repeats Detected in Prokaryotic Genomes

Genomes contain many perfect and approximate tandem repeats (TRs) which are two or more adjacent similar DNA sequences of a certain length and are products of tandem duplication. Duplication generally requires small non-duplicated repeats as primers [1]. Present techniques for finding TRs are divided into fully automated techniques such as the Tandem Repeats Finder (TRF) [2], TROLL and Sputnik, and visualization techniques such as REPuter and FORRepeats. The fully automated techniques are not suitable for detecting the TRs with a long period and a low identity. So, we use the color-coding method (CC) that is suitable for detecting local repetitive structures such as TRs [4]. The CC method is a visualization technique in which nucleotides are substituted by squares filled with user-defined colors in accordance with a nucleotide type, and the color-coded sequence is aligned into two dimensions with a column width. When a TR exists in the sequence, the TR can be detected as a recognizable pattern. In this study, we detect the TRs from 44 prokaryotic genomes using CC. In order to clarify the advantages of CC, we compare the results detected by CC and TRF in D. radiodurans, H. influenzae and Y. pestis. In addition, by visualizing the results obtained with TR similarity search, we examine TR structures detected by CC.