- Search Result
- Database Details
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.
- 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
Multiple search: Yes
Download: FASTA, Other.
Genomic Overview: No