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/.