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Nucleic Acids Research 2006 34(Database Issue):D145-D149; doi:10.1093/nar/gkj084
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Nucleic Acids Research, 2006, Vol. 34, Database issue D145-D149
© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

MODOMICS: a database of RNA modification pathways

Stanislaw Dunin-Horkawicz1, Anna Czerwoniec2, Michal J. Gajda1, Marcin Feder1, Henri Grosjean3 and Janusz M. Bujnicki1,2,*

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, Poland 3Laboratoire d'Enzymologie et Biochimie Structurales, CNRS Bld 34, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France

*To whom correspondence should be addressed. Tel: +48 22 597 0750; Fax: +48 22 597 0715; Email: iamb{at}genesilico.pl

Received August 15, 2005. Accepted October 12, 2005.

MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It 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. The current list of modifications and pathways is comprehensive, while the dataset of enzymes is limited to Escherichia coli and Saccharomyces cerevisiae and sequence alignments are presented only for tRNAs from these organisms. RNAs and enzymes from other organisms will be included in the near future. 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/.

Correspondence may also be addressed to Henri Grosjean. Tel: +33 1 6982 3468, Fax: +33 1 6982 3129; Email: henri.grosjean{at}lebs.cnrs-gif.fr

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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