tRNAdb 2009: compilation of tRNA sequences and tRNA genes

• Published in: Nucleic acids research Vol. 37; no. suppl-1; pp. D159 - D162
• Main Authors: Jühling, Frank, Mörl, Mario, Hartmann, Roland K, Sprinzl, Mathias, Stadler, Peter F, Pütz, Joern
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-01-2009; Oxford Publishing Limited (England)
• Subjects: Biochemistry, Molecular Biology; Cellular Biology; Databases, Nucleic Acid; Life Sciences; Phylogeny; RNA, Transfer - chemistry; RNA, Transfer - classification; RNA, Transfer - genetics; Sequence Analysis, DNA; Sequence Analysis, RNA; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn772

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.