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Figure 3 | BMC Genomics

Figure 3

From: Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

Figure 3

T. maritima tetranucleotide MCM, ROF, and ZOM autocorrelation profiles. Di-, tetra- and hexanucleotide ZOMs (top), respectively red, green and blue lines, together with tetranucleotide MCM and ROF (bottom), respectively green and red lines, based autocorrelation profiles of T. maritima. Autocorrelation scores (vertical axis) were obtained with 5 kbp sliding windows, overlapping every 2.5 kbp, correlated with mean genomic values. The horizontal axis represents chromosomal position, with each point spanning 5 kbp. All large dips, except the one found at position 190 kbp, which was found to be 16S, 23S and 5S rRNA genes, are presumed to be horizontally transferred. The marked dips in the tetranucleotide ZOM profiles are part of a presumed horizontally acquired ABC transport system. It can be observed from the Figure that the profile based on tetranucleotide ROFs resembles the ZOM profiles, but that some dips are less visible. The low average autocorrelation value in the tetranucleotide MCM profile is assumed to be caused by lower departure values between observed and expected tetranucleotide frequencies due to small sliding window size. Although many of the large dips found in the other measures were absent in the MCM profile, irregularities (marked dots) were observed in the MCM profile that were not easily detectable with the other measures. Looking at the di-, tetra- and hexanucleotide ZOM profiles, progressively more fluctuations can be observed for increasing oligonucleotide size while average autocorrelation scores drop.

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