Evaluation of the color-coding method for searching tandem repeats in prokaryotic genomes

Abstract

By using the color-coding (CC) method, which is based on visual inspection by eyes, tandem repeats (TRs) were searched in the Yersinia pestis, Deinococcus radiodurans and Haemophilus influenzae genomes by three independent inspectors, and the detected TRs were compared to investigate the individual variations among inspectors in detecting TRs. We also compared the CC method with Tandem Repeats Finder (TRF) that is one of the algorithmic methods for searching TRs, in the detection ability of TRs, demonstrating that the CC method can get much larger number of TRs than TRF, even long TRs with much lower sequence identity.