tRNAdb 2009: compilation of tRNA sequences and tRNA genes

By Frank Jühling, M. Mörl, R. Hartmann, M. Sprinzl, Peter F. Stadler, J. Pütz. Nucleic Acids Res., 2008

791 citations recorded by the source corpus.

One of the first specialized collections of nucleic acid sequences in life sciences was the ‘compilation of tRNA sequences and sequences of tRNA genes’ (http://www.trna.uni-bayreuth.de). Here, an updated and completely restructured version of this compilation is presented (http://trnadb.bioinf.uni-leipzig.de). The new database, tRNAdb, is hosted and maintained in cooperation between the universities of Leipzig, Marburg, and Strasbourg. Reimplemented as a relational database, tRNAdb will be updated periodically and is searchable in a highly flexible and user-friendly way. Currently, it contains more than 12 000 tRNA genes, classified into families according to amino acid specificity. Furthermore, the implementation of the NCBI taxonomy tree facilitates phylogeny-related queries. The database provides various services including graphical representations of tRNA secondary structures, a customizable output of aligned or un-aligned sequences with a variety of individual and combinable search criteria, as well as the construction of consensus sequences for any selected set of tRNAs.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f624e452a693107c05cf684c2de0339a20eae931

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In Molecular Biology

Citations in the corpus

MODOMICS: a database of RNA modification pathways—2013 update (2012, methodology): “In particular, in addition to the previously collected manually curated sequences, MODOMICS contains now all tRNAs imported from the Transfer RNA database (33), which were found to possess modified nucleosides (over 500 tRNA sequences in total).”
Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine (2022, background): “In bacteria and eukaryotes, A-to-I editing occurs at the wobble position in a subset of tRNAs, thereby expanding their decoding capacity (Crick, 1966; Juhling et al., 2009; Murphy and Ramakrishnan, 2004).”
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA (2012, methodology): “(A) Plot of conversion against read coverage at 28 known m(5)C sites in human tRNAs (43).”
ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, background): “For representation at the sequence level, one-letter abbreviations for some modified bases have been introduced by Sprinzl and coworkers (37), but the number of currently known modifications exceeds the number of letters in the Latin alphabet.”