REDIdb: an upgraded bioinformatics resource for organellar RNA editing

RNA editing is a post-transcriptional molecular process whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. Editing sites are currently annotated in primary databases such as GenBank, even though a specific descriptor for RNA editing is not one of the features of the actual flat-files. As a consequence, editing modifications are annotated under “misc_feature” or in the notes indicating the existence of RNA editing alterations, but omitting important details such as the editing type or the nucleotide positions affected. A systematic study of known and experimentally determined RNA editing events is, thus, time-consuming and sometimes precluded by annotation errors in Genebank flat-files. With the aim to improve the annotation status of RNA editing sites, we developed a specialized database, called REDIdb, devoted to store and give access to editing events in organelles and especially in mitochondria. Since its first release, REDIdb has been updated and upgraded with a refurbished web-interface in addition to graphical and computational facilities that improve RNA editing investigations. Presently REDIdb stores 10,600 editing positions distributed over 828 organellar sequences. Moreover 65% of all events are located in the mitochondrion and about 62% are C-to-U conversions. Editing sites are annotated in their biological context, organized in GenBank-like flatfiles and downloadable in different formats. In protein coding genes, the user can visualize known domains and editing sites falling in such domains. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/.