Compilation of tRNA sequences and sequences of tRNA genes

By M. Sprinzl, K. Vassilenko. Nucleic Acids Res., 2004

918 citations recorded by the source corpus.

Maintained at the Universität Bayreuth, Bayreuth, Germany, the Compilation of tRNA Sequences and Sequences of tRNA Genes is accessible at the URL http://www.tRNA.uni-bayreuth.de with mirror site located at the Institute of Protein Research, Pushchino, Russia (http://alpha.protres.ru/trnadbase). The compilation is a searchable, periodically updated database of currently available tRNA sequences. The present version of the database contains a new Genomic tRNA Compilation including the sequences of tRNA genes from genomic sequences published up to July 2003. It consists of about 5800 tRNA gene sequences from 111 organisms covering archaea, bacteria, higher and lower eukarya. The former Compilation of tRNA Genes (up to the end of 1998) and the updated Compilation tRNA Sequences (561 entries) are also supported by the new software. The database can be explored by using multiple search criteria and sequence templates. The database provides a service that allows to obtain statistical information on the occurrences of certain bases at given positions of the tRNA sequences. This allows phylogenic studies and search for identity elements in respect to interactions of tRNAs with various enzymes.

Subfields: Molecular Biology

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Citations in the corpus

GtRNAdb: a database of transfer RNA genes detected in genomic sequence (2008, background): “For comparison to older reference tRNA sequences, multiple alignments also include aligned entries from the original Sprinzl tRNA database (10), when present from the same species and isotype.”
MODOMICS: a database of RNA modification pathways (2005, methodology): “We have collected all the currently known RNA modifications from the RNAMods database (2) and the tRNA sequences from the Bayreuth database (3).”
MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, background): “The total size of the sequence databases (NCBI [7,8], EMBL [9], DDBJ [10], JGI [11], RDP [12], Swiss-Prot/TrEMBL [13], CRW [14], Bayreuth tRNA compila-tions [15], and the Genomic tRNA Database [16]) is several orders of magnitude greater than that of the structure databases.”
Pfold: RNA secondary structure prediction using stochastic context-free grammars (2003, methodology): “Examples of such conserved structures are found in tRNA (1), rRNA (2,3), tmRNA (4), RNase P RNA (5) and SRP RNA (6).”
A statistical sampling algorithm for RNA secondary structure prediction. (2003, background): “tRNA database (2) is warranted to assess the degree of generality of such predicted anticodon accessibility.”
Reconstruction of Biochemical Networks in Microbial Organisms (2008, background): “Challenges that are unique to reconstruction of TR–TR networks include reaction mechanisms of certain modifications (for example, tRNA modification”
RNAstructure: web servers for RNA secondary structure prediction and analysis (2013, neutral): “This sequence is the tRNA RA7680 from the Sprinzl database (41).”
Tissue-Specific Differences in Human Transfer RNA Expression (2006, background): “Enthusiasm for tackling this challenge was low because prior to the human genome sequencing project, human tRNAs were considered to be no more diverse than those in unicellular organisms [8,9].”
RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. (2008, background): “Notably, m1G9 is frequently found in animal but not in yeast or plant mitochondrial tRNAs (Sprinzl and Vassilenko, 2005), and preliminary evidence indeed suggests that MRPP1 functions in the m1G9 methylation of human mitochondrial tRNAs (C. Nachbagauer, J.H., and W.R., unpublished data).”
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. (2004, methodology): “Example output of the computer program ARAGORN from a search of eubacterial tRNA genes in the Sprinzl database (12).”
tRNAdb 2009: compilation of tRNA sequences and tRNA genes (2008, methodology): “The tRNAdb, with one of the largest numbers of entries among RNA databases, is not only an excellent model system for implementing and validating algorithms and processes of automated nucleic acid data transfer, but also for the development of novel sequence analysis tools (1).”
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. (2005, methodology): “From publicly available databases (Larsen and Zwieb 1991; Sprinzl et al. 1998; Brown 1999; Cannone et al. 2002; Alm Rosenblad et al. 2003; Zwieb et al. 2003), we took samples of sequences for diverse types of structural RNAs with secondary structures determined by comparative sequence analysis.”
MODOMICS: a database of RNA modification pathways. 2008 update (2008, methodology): “Recently, we have expanded our database to include further tRNA and tDNA sequences from the Bayreuth database (12), with modifications curated manually, and rRNA sequences from the Comparative RNA Website (13).”
Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [Topt], 23°C) and Stetteria hydrogenophila (Topt, 95°C) (2003, background): “The posttranscriptional processing of tRNA produces a diverse wealth of modified nucleotides (29, 30, 41), most of which occur at conserved RNA sequence locations in all three phylogenetic domains (4, 45).”