Bioinformatic tools for DNA methylation and histone modification: A survey.

Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organisms. Computational approaches have enabled us to analyze mass data produced by these methods. Next-generation sequencing (NGS) methods have been broadly used to identify these target sites and their patterns. By using these patterns, the emergence of diseases could be prognosticated. In this study, target site prediction tools for two major epigenetic mechanisms comprising histone modification and DNA methylation are reviewed. Publicly accessible databases are reviewed as well. Some suggestions regarding the state-of-the-art methods and databases have been made, including examining patterns of epigenetic changes that are important in epigenotypes detection. • A comparison was made between tools to predict the DNA methylation and histone modification • Epigenetic sites are not adequately performed in mitochondria and cytoplasm • DNA methylation and histone modification were reviewed • It is recommended simultaneous emergence of DNA methylation and post-translational histone modification • Suggestions have been made about the state-of-the-art methods and databases. [ABSTRACT FROM AUTHOR]