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MODOMICS: a database of RNA modification pathways. 2008 update
Open accessAbstract
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.
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A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
Roberts, R. J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg274 · Cited by 755
Cited by
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Dominissini, D., Moshitch-Moshkovitz, S., Schwartz, S., Salmon-Divon, M., Ungar, L., Osenberg, S., Cesarkas, K., Jacob-Hirsch, J., Amariglio, N., Kupiec, M., et al. (2012) · Nature · doi:10.1038/nature11112 · Cited by 4,884
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,371
The RNA modification database, RNAMDB: 2011 update
Cantara, W. A., Crain, P. F., Rozenski, J., McCloskey, J. A., Harris, K. A., Zhang, X., Vendeix, F. A. P., Fabris, D., & Agris, P. F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1028 · Cited by 820
Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N., & Rechavi, G. (2013) · Nature Protocols · doi:10.1038/nprot.2012.148 · Cited by 710
Motorin, Y., & Helm, M. (2011) · WIREs RNA · doi:10.1002/wrna.79 · Cited by 441
Metadata
- Authors
- Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K. H., Kasprzak, J. M., Bujnicki, J. M., Grosjean, H., & Rother, K.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D118-D121
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2396466193
- Cited by
- 199
- References
- 1
- FWCI
- 6.58
- Type
- journal article
- Language
- en
- Open access
- gold
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- Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K. H., Kasprzak, J. M., Bujnicki, J. M., Grosjean, H., & Rother, K. (2009). MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkn710
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