Document Type
Article
Original Publication Date
2009
Journal/Book/Conference Title
BMC Bioinformatics
Volume
10
DOI of Original Publication
10.1186/1471-2105-10-65
Date of Submission
August 2014
Abstract
Background CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. (2006) recently developed a new algorithm, CpGcluster, which uses a completely different mathematical approach from previous traditional algorithms. Their evaluation suggests that CpGcluster provides a much more efficient approach to detecting functional clusters or islands of CpGs.
Results We systematically compared CpGcluster with the traditional algorithm by Takai and Jones (2002). Our comparisons of (1) the number of islands versus the number of genes in a genome, (2) the distribution of islands in different genomic regions, (3) island length, (4) the distance between two neighboring islands, and (5) methylation status suggest that Takai and Jones' algorithm is overall more appropriate for identifying promoter-associated islands of CpGs in vertebrate genomes.
Conclusion The generation of genome sequence and DNA methylation data is expected to accelerate greatly. The information in this study is important for its extensive utility in gene feature analysis and epigenomics including gene prediction and methylation chip design in different genomes.
Rights
© 2009 Han and Zhao; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Is Part Of
VCU Psychiatry Publications
Comparison of the length distribution of CGIs and CGCs. This file includes the comparison of the length distribution of CGIs and CGCs in the human and mouse genomes.
1471-2105-10-65-s2.pdf (26 kB)
Figure S2. Figure S2 displays the distribution of distance between two neighboring CGCs in the promoter region of human-mouse homologous genes.
Comments
Originally published at http://dx.doi.org/10.1186/1471-2105-10-65