DNAmod: the DNA modification database
Abstract Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain vari...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-019-0349-4 |
| _version_ | 1818842737210818560 |
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| author | Ankur Jai Sood Coby Viner Michael M. Hoffman |
| author_facet | Ankur Jai Sood Coby Viner Michael M. Hoffman |
| author_sort | Ankur Jai Sood |
| collection | DOAJ |
| description | Abstract Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain various other modified DNA nucleobases. Numerous databases describe RNA and histone modifications, but no database specifically catalogues DNA modifications, despite their broad importance in epigenetic regulation. To address this need, we have developed DNAmod: the DNA modification database. DNAmod is an open-source database (https://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 these 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. |
| first_indexed | 2024-12-19T04:46:44Z |
| format | Article |
| id | doaj.art-4beaf534f90a40029cceef5b635b7f97 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-19T04:46:44Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-4beaf534f90a40029cceef5b635b7f972022-12-21T20:35:27ZengBMCJournal of Cheminformatics1758-29462019-04-0111111010.1186/s13321-019-0349-4DNAmod: the DNA modification databaseAnkur Jai Sood0Coby Viner1Michael M. Hoffman2Department of Medical Biophysics, University of TorontoPrincess Margaret Cancer CentreDepartment of Medical Biophysics, University of TorontoAbstract Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain various other modified DNA nucleobases. Numerous databases describe RNA and histone modifications, but no database specifically catalogues DNA modifications, despite their broad importance in epigenetic regulation. To address this need, we have developed DNAmod: the DNA modification database. DNAmod is an open-source database (https://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 these 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.http://link.springer.com/article/10.1186/s13321-019-0349-4DNA modificationsNucleobasesEpigenomics |
| spellingShingle | Ankur Jai Sood Coby Viner Michael M. Hoffman DNAmod: the DNA modification database Journal of Cheminformatics DNA modifications Nucleobases Epigenomics |
| title | DNAmod: the DNA modification database |
| title_full | DNAmod: the DNA modification database |
| title_fullStr | DNAmod: the DNA modification database |
| title_full_unstemmed | DNAmod: the DNA modification database |
| title_short | DNAmod: the DNA modification database |
| title_sort | dnamod the dna modification database |
| topic | DNA modifications Nucleobases Epigenomics |
| url | http://link.springer.com/article/10.1186/s13321-019-0349-4 |
| work_keys_str_mv | AT ankurjaisood dnamodthednamodificationdatabase AT cobyviner dnamodthednamodificationdatabase AT michaelmhoffman dnamodthednamodificationdatabase |