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DNAmod: the DNA modification database

By Ankur Jai Sood, Coby Viner, Michael M. Hoffman

Posted 26 Aug 2016
bioRxiv DOI: 10.1101/071712 (published DOI: 10.1186/s13321-019-0349-4)

Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain various modified DNA nucleobases, including several in which one base is largely or entirely replaced by a particular covalent modification. Numerous databases describe RNA and histone modifications, but no database specifically catalogues DNA modifications, despite their broad importance as an element of epigenetic regulation. To address this need, we have developed DNAmod: the DNA modification database. DNAmod is an open-source database (http://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. DNAmod provides a web interface to easily browse and search through its modifications. The database annotates the chemical properties and structures of all curated modified DNA bases, and a much larger list of candidate chemical entities. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.

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