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Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.

Chae H, Park J, Lee SW, Nephew KP, Kim S - Nucleic Acids Res. (2013)

Bottom Line: First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes.Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers.In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA.

ABSTRACT
CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

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Get common k-mer(flank) exist in all the species. Each alphabet stands for the k-mer(flank) sequences. Based on the k-mer(flank) rank order in common, k-mer(flank) order in each species are set. Rank difference between common and other species are computed.
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gkt144-F2: Get common k-mer(flank) exist in all the species. Each alphabet stands for the k-mer(flank) sequences. Based on the k-mer(flank) rank order in common, k-mer(flank) order in each species are set. Rank difference between common and other species are computed.

Mentions: Once the common k-mers/k-flanks are collected, they are sorted according to their frequencies. Based on the ranks of common k-mers/k-flanks, their ranks are marked. Since these k-mers/k-flanks are in common across all 10 mammalian genomes, the order of k-mers/k-flanks in each species becomes a permutation of ranks of common k-mers/k-flanks. This k-mer/k-flank ranking method based on the common k-mer/k-flank ranks comes from an assumption that all these mammalian species are closely related from the evolutionary perspective. Figure 2 illustrates the experimental protocol.Figure 2.


Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.

Chae H, Park J, Lee SW, Nephew KP, Kim S - Nucleic Acids Res. (2013)

Get common k-mer(flank) exist in all the species. Each alphabet stands for the k-mer(flank) sequences. Based on the k-mer(flank) rank order in common, k-mer(flank) order in each species are set. Rank difference between common and other species are computed.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643570&req=5

gkt144-F2: Get common k-mer(flank) exist in all the species. Each alphabet stands for the k-mer(flank) sequences. Based on the k-mer(flank) rank order in common, k-mer(flank) order in each species are set. Rank difference between common and other species are computed.
Mentions: Once the common k-mers/k-flanks are collected, they are sorted according to their frequencies. Based on the ranks of common k-mers/k-flanks, their ranks are marked. Since these k-mers/k-flanks are in common across all 10 mammalian genomes, the order of k-mers/k-flanks in each species becomes a permutation of ranks of common k-mers/k-flanks. This k-mer/k-flank ranking method based on the common k-mer/k-flank ranks comes from an assumption that all these mammalian species are closely related from the evolutionary perspective. Figure 2 illustrates the experimental protocol.Figure 2.

Bottom Line: First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes.Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers.In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA.

ABSTRACT
CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.

Show MeSH