NAR Molecular Biology Database Collection entry number 840

http://genesilico.pl/modomics/

Dunin-Horkawicz S.¹, Czerwoniec A.², Gajda M.J.¹, Feder M.¹, Grosjean H.³, and Bujnicki J.M.^1,2

¹Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology ul. Ks., Trojdena 4, PL-02-190 Warsaw, Poland
²Bioinformatics Laboratory, Institute for Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland³Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bld. 34, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France

Contact iamb@genesilico.pl

MODOMICS (‘omics’ approach to RNA modification) integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. MODOMICS can be queried by the type of nucleoside (e.g. A, G, C, U, I, m1A, nm5s2U etc.), type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literature data. The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/.

The current list of modifications and pathways is comprehensive. The dataset of enzymes is limited to Escherichia coli and Saccharomyces cerevisiae and sequence alignments (and localization of modified nucleosides) are available only for tRNAs from these organisms. tRNAs and enzymes from other organisms as well as other RNAs will be included in the near future.

MODOMICS would not be possible without the data from publicly available databases, in particular the RNAMods database and the Bayreuth tRNA dataset. We are grateful to Daylight Chemical Information Systems Inc. for providing their SMI2GIF service. Our work is supported by the EMBO/HHMI Young Investigator Programme award to J.M.B. S.D.H. was supported by the NIH (grant 5R01AI056034-02). Travel expenses between Poland and France were covered by EGIDE (Polonium grant #07558WK) and by the CEMBM Center of Excellence grant from the 5th Framework Programme of the European Union (contract #QLK6-CT-2002-90363).

1. Bujnicki J.M., Droogmans L., Grosjean H., Purushothaman S.K., Lapeyre B. (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag.
2. Dunin-Horkawicz S., Czerwoniec A., Gajda M.J., Feder M., Grosjean H., Bujnicki J.M. (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res Database Issue (in press).

Go to the abstract in the NAR 2006 Database Issue.

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