tRNAdb

Database version: 2009

RNA Type: Multiple classes

Overview: 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.

Search Methods:

• Keyword: Class or Order or Family or Species: strain: or NCBI-ID of taxon, Anticodon, sequence, structure, pubmed ID, reference
• Similarity: BLAST by sequence
• TAG: Taxonomy tree, tRNA gene/sequence, plastids, mitochondria, organisms or viruses, amino acid

Source: Besides the imported data sets, 255 new tRNA gene sequences retrieved from a series of completed archaeal genomes recently submitted to NCBI (Methanococcus aeolicus Nankai-3, Methanosarcina acetivorans C2A, Methanospirillum hungatei JF-1, Nanoarchaeum equitans Kin4-M, Staphylothermus marinus F1 and Sulfolobus acidocaldarius DSM 639) were scanned by tRNAscan-SE (4) and imported using a new data input interface directly connected to the database. For reasons of clarity and compatibility, all sequences are presented in the alignment format of the Mamit-tRNA database (3), including a structural annotation generated from the assignment of nucleotide position numbers. Currently, the data set contains 12 099 sequences from tRNA genes (577 organisms) and 623 tRNA sequences (104 organisms).

Information Source: In silico annotation.

Information Content: Database, Sequence, Structure, Taxonomy.

Reference: Jühling et al., 2009

PubmedID: 18957446.

Year: 2009

Multiple search: Yes

Download: FASTA, Other.

Genomic Overview: No

Organism: Prochlorococcus marinus, Moloney murine leukemia virus, Bacillus thuringiensis serovar konkukian str. 97-27, Pyrobaculum aerophilum str. IM2, Fusobacterium nucleatum subsp. nucleatum ATCC 25586, Symbiobacterium thermophilum IAM 14863, Leifsonia xyli subsp. xyli str. CTCB07, Oceanobacillus iheyensis HTE831, Streptococcus mutans UA159, Nanoarchaeum equitans Kin4-M, Bacillus cereus ATCC 10987, Nostoc sp. PCC 7120, Enterococcus faecalis V583, Clostridium perfringens str. 13, Methanopyrus kandleri AV19 and 148 others.

Url: http://trnadb.bioinf.uni-leipzig.de