tDRnamer: standardized naming for tRNA-derived RNAs
Transfer RNA, well-studied as the key adapter molecule in protein translation, is now recognized as having a plethora of additional regulatory functions when further processed into shorter RNAs. Many groups have contributed to this rapidly advancing field, inevitably leading to a constellation of diverse yet often overlapping names attributed to tRNA-derived fragments (e.g., tRFs, tsRNAs, tiRNAs, SHOT-RNAs, tRNA halves, etc.). In order to promote the growth of the research community and aid the recognition of structural/processing/functional relationships among the many forms of tRNA-derived RNAs, the tRNA community is proposing a consistent, uniform naming system integrating three main parts: (i) the prefix "tDR" (tRNA-Derived RNA), (ii) the portion of the mature tRNA from which the fragment is derived (using standardized Sprinzl tRNA base numbering), and (iii) the Genomic tRNA Database Identifier (GtRNAdb ID) of the tRNA gene(s) or transcript(s). tDRnamer provides a consistent, stable name for submitted tDR sequences based on this naming system. It also gives additional annotation for each submitted tDR sequence including length, secondary structure, stem and loop features overlapping the tDR, and all possible mature tRNAs that could have produced the tDR. Moreover, users can submit tDR names that are formatted according to this naming system and obtain the corresponding sequences with related annotations.
tDRnamer is a web-based application that only requires to be used with a web browser. No software installation is needed. This user guide provides the details of the standardized tDR naming system and the walk-through of using this application that can be accessed here.