title: tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs.
abstract: tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as a web server at http://genesilico.pl/trnamodpred/.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Magdalena A
authors.initials: MA
authors.lastname: Machnicka
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.affiliation: Department of Microbiology and Cell Science, University Florida, Gainesville, FL, USA.
authors.forename: Valérie
authors.initials: V
authors.lastname: de Crécy-Lagard
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland. Electronic address: iamb@genesilico.pl.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics*
chemical_list: D012343:RNA, Transfer
keywords: Bioinformatics; Homology; MODOMICS; RNA modification; Sequence similarity; tRNA