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Information


Unique identifier OMICS_09913
Name tRNAdb
Alternative name Transfer RNA database
Restrictions to use None
Maintained Yes

Publication for Transfer RNA database

tRNAdb citations

 (4)
library_books

Dynamics of tRNA fragments and their targets in aging mammalian brain

2016
F1000Res
PMCID: 5224686
PMID: 28105302
DOI: 10.5256/f1000research.10897.r17976

[…] nalysis. We collapsed and mapped the reads to the rat genome (rn6, http://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/), and also to the union of rat tRNAs from two independent databases ( http://gtrnadb.ucsc.edu and http://trnadb.bioinf.uni-leipzig.de, also including mitochondrial tRNA genes from the latter) using Bowtie (version 1.1.1, released on 10/1/2014, http://bowtie-bio.sourceforge.net/ […]

call_split

Novel Centromeric Loci of the Wine and Beer Yeast Dekkera bruxellensis CEN1 and CEN2

2016
PLoS One
PMCID: 4999066
PMID: 27560164
DOI: 10.1371/journal.pone.0161741
call_split See protocol

[…] y GIRI (Genetic Information Research Institute, http://www.girinst.org) and EMBOSS explorer (http://emboss.bioinformatics.nl/cgi-bin/emboss/palindrome). We searched for the tRNA gene sequences in the transfer RNA database (http://trna.bioinf.uni-leipzig.de/DataOutput/Search).To determine the frequency of appearance, the sequences of cloned centromeres were searched against the assembled scaffolds […]

library_books

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

2014
BMC Genomics
PMCID: 4169805
PMID: 25189468
DOI: 10.1186/1471-2164-15-760

[…] and adapter sequences from the Solexa sequencing reads, unique sequences of 17–35 nt were used for further analysis. First, the unique sequences were queried against ribosomal and transfer RNAs from tRNAdb (http://trna.bioinf.uni-leipzig.de/DataOutput/Search), SILVArRNA (http://www.arb-silva.de/), and NONCODE v3.0 (http://www.noncode.org/NONCODERv3/; plant database only, single-nt mismatches allo […]

library_books

Analysis of the melon (Cucumis melo) small RNAome by high throughput pyrosequencing

2011
BMC Genomics
PMCID: 3163571
PMID: 21812964
DOI: 10.1186/1471-2164-12-393

[…] sition were considered. Known sRNAs were identified by searching public databases using BLAST version 2.2.19 [] and allowing up to two mismatches. The following databases and sequences were searched: Transfer RNA Database (version 2009) [], Plant Small Nucleolar RNA Database (v1.2) [], SILVA (ribosomal RNA database, v100) [], The Arabidopsis Small RNA Project (ASRP) Database [], Rfam Database 10.0 […]

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tRNAdb institution(s)
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

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