Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation Gómez Martín, Cristina Lebrón, Ricardo Oliver Jiménez, José Lutgardo Hackenberg, Michael CpG islands clustering DNA words DNA methylation Virtual Machine The promoter region of around 70% of all genes in the human genome is overlapped by a CpG island (CGI). CGIs have known functions in the transcription initiation and outstanding compositional features like high GþC content and CpG ratios when compared to the bulk DNA. We have shown before that CGIs manifest as clusters of CpGs in mammalian genomes and can therefore be detected using clustering methods. These techniques have several advantages over sliding window approaches which apply compositional properties as thresholds. In this protocol we show how to determine local (CpG islands) and global (distance distribution) clustering properties of CG dinucleotides and how to generalize this analysis to any k-mer or combinations of it. In addition, we illustrate how to easily cross the output of a CpG island prediction algorithm with our methylation database to detect differentially methylated CGIs. The analysis is given in a step-by-step protocol and all necessary programs are implemented into a virtual machine or, alternatively, the software can be downloaded and easily installed. 2026-02-20T11:08:02Z 2026-02-20T11:08:02Z 2018-04-01 book part Gómez-Martín, C., Lebrón, R., Oliver, J.L., Hackenberg, M. (2018). Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation. In: Vavouri, T., Peinado, M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7768-0_3 https://hdl.handle.net/10481/111304 10.1007/978-1-4939-7768-0_3 eng Methods in Molecular Biology; http://creativecommons.org/licenses/by-nc-nd/4.0/ embargoed access Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Attribution-NonCommercial-NoDerivatives 4.0 Internacional Springer Nature