Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-0

0% GC content. The comparisons were performed to test the reliability of different oligonucleotide based statistical measures consisting of di- to hexanucleotide ZOMs, tetranucleotide ROFs and MCMs. The chromosomes and plasmids, represented as points along the horizontal axis, were correlated with the random DNA sequence, with the corresponding correlation scores on the vertical axis, and sorted by increasing AT content from left to right. Higher correlation scores means better match. In (A) all chromosomes and plasmids were compared using di- to hexanucleotide ZOMs, while in (B) they were compared using tetranucleotide ROFs and MCMs, with tetranucleotide ZOMs included as reference. It can be observed that dinucleotide ZOMs achieve surprisingly high correlation scores (A) while hexanucleotide ZOMs show no correlation at all. Tetranucleotide ROFs (B) achieves slightly higher correlation values than both tetranucleotide MCMs and ZOMs.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-5

Ion values (black dots) were then compared with host average autocorrelation values (expected plasmid-host correlation score, red line) based on 40 kbp sliding windows and tetranucleotide ZOMs. The green line represents lower autocorrelation values, i.e. average autocorrelation values subtracted by standard deviation, while the blue and cyan lines show host and plasmid GC content respectively. The vertical axis represents host bacteria average autocorrelation values (red line), host GC content (blue line), plasmid GC content (cyan), and plasmid-host correlations (black dots). All bacteria and archaea with corresponding plasmids are distributed as points along the horizontal axis and sorted by increasing plasmid GC content from left to right. From the graph it can be observed that GC rich bacteria were more similar to their plasmids in terms of tetranucleotide ZOMs than AT rich bacteria. It can also be noticed that average autocorrelation scores (expected plasmid-host correlation scores) seems to increase and become less volatile for GC rich bacteria than their AT rich counterparts.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-6

0% GC content. The comparisons were performed to test the reliability of different oligonucleotide based statistical measures consisting of di- to hexanucleotide ZOMs, tetranucleotide ROFs and MCMs. The chromosomes and plasmids, represented as points along the horizontal axis, were correlated with the random DNA sequence, with the corresponding correlation scores on the vertical axis, and sorted by increasing AT content from left to right. Higher correlation scores means better match. In (A) all chromosomes and plasmids were compared using di- to hexanucleotide ZOMs, while in (B) they were compared using tetranucleotide ROFs and MCMs, with tetranucleotide ZOMs included as reference. It can be observed that dinucleotide ZOMs achieve surprisingly high correlation scores (A) while hexanucleotide ZOMs show no correlation at all. Tetranucleotide ROFs (B) achieves slightly higher correlation values than both tetranucleotide MCMs and ZOMs.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-1

(below), respectively green and red lines, based autocorrelation profiles of . Autocorrelation scores (vertical axis) are 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. Average autocorrelation scores drop progressively for di- to hexanucleotide ZOMs, presumably due to lower departure values between observed and expected tetranucleotide frequencies caused by small sliding windows. ZOM and ROF based profiles appear similar, but the former appear more detailed. Although the hexanucleotide ZOM and tetranucleotide MCM measures had similar average autocorrelation scores, the latter can be observed to vary considerably more than the former. All marked dots represent presumed horizontally acquired DNA, and the two largest dips located close to 2.2 mbp and 2.7 mbp are known prophages.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-4

Isting of heptanucleotide frequencies taken from 5 kbp of DNA consisting of 16S, 23S and 5S rRNA genes. The horizontal axis represents nucleotide positions, each point spanning 1 kbp, in the chromosome, while the vertical axis gives correlation values based on comparisons between the sliding window and the DNA vector. The marked peak indicates the closest hit, containing corresponding rRNA genes in . Although is very distantly related to (hexanucleotide ZOM score of 0.13) its rRNA genes could be detected using DNA from the corresponding rRNA genes with the search method based on ROFs.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes-2

F (bottom), respectively green and red lines, based autocorrelation profiles of . 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.<p><b>Copyright information:</b></p><p>Taken from "Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/104</p><p>BMC Genomics 2008;9():104-104.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2289816.</p><p></p

System dynamics mental models (developed using Stella Professional).

<p>System dynamics mental models (developed using Stella Professional).</p

Agenda for SGMB workshop.

<p>Agenda for SGMB workshop.</p

Map of Monze District.

<p>Reprinted from [Zambia_Mosaic_250Karc1950_ddecw] under a CC BY licence, with permission from the Surveyor General, Government Republic of Zambia, original copyright, [1974].</p

Map of Lundazi District based on the LayerStack process (developed by authors).

<p>Reprinted from [Zambia_Mosaic_250Karc1950_ddecw] under a CC BY licence, with permission from the Surveyor General, Government Republic of Zambia, original copyright, [1974].</p