Color-coding reveals tandem repeats in the Escherichia coli genome.
Genomic DNA contains a wide variety of repetitive sequences. In Escherichia coli, there have been several classes of repetitive sequences reported, some of which cluster as tandem repeats. We propose a novel method for analyzing symbolic sequences by two-dimensional pattern formation with color-coding. We applied this method for searching tandem repeats in the E. coli genome and found approximately 50 repeats with periods longer than 30 bases. The longest repeat has a period of 1267 bases.
Yoshida
T
T
Graduate School of Mathematics, Nagoya University, Nagoya, Chikusa-ku, 464-8602, Japan.
Obata
N
N
Oosawa
K
K
D001483:Base Sequence; D003116:Color; D019295:Computational Biology / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D017422:Sequence Analysis, DNA / Q000379:methods*; D020080:Tandem Repeat Sequences / Q000235:genetics*
D004269:DNA, Bacterial