title: MODOMICS: a database of RNA modification pathways--2013 update.
abstract: MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue of 'building blocks' for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
authors.forename: Magdalena A
authors.initials: MA
authors.lastname: Machnicka
authors.forename: Kaja
authors.initials: K
authors.lastname: Milanowska
authors.forename: Okan
authors.initials: O
authors.lastname: Osman Oglou
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Purta
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Kurkowska
authors.forename: Anna
authors.initials: A
authors.lastname: Olchowik
authors.forename: Witold
authors.initials: W
authors.lastname: Januszewski
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kalinowski
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.forename: Kristian M
authors.initials: KM
authors.lastname: Rother
authors.forename: Mark
authors.initials: M
authors.lastname: Helm
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.forename: Henri
authors.initials: H
authors.lastname: Grosjean
mesh_terms: D030561:Databases, Nucleic Acid; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D020407:Internet; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D004798:Enzymes; D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; D012313:RNA