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sRNATarBase specifications


Unique identifier OMICS_11142
Name sRNATarBase
Restrictions to use None
Data access File download, Browse
Version 3.0
Maintained No


This tool is not available anymore.

Publications for sRNATarBase

sRNATarBase citations


Global Screening of Salmonella enterica Serovar Typhimurium Genes for Desiccation Survival

Front Microbiol
PMCID: 5596212
PMID: 28943871
DOI: 10.3389/fmicb.2017.01723

[…] ble ). To determine if any of these intergenic regions encode non-coding sRNA, genomic DNA sequence was extracted for these intergenic regions and blasted for the presence of small RNA (sRNA) against sRNATarBase 2.0, a database of bacterial sRNA targets verified by experiment (Cao et al., ). However, we could not find hit for any known sRNA. There might be novel genetic elements in these intergeni […]


Mycoplasma non coding RNA: identification of small RNAs and targets

BMC Genomics
PMCID: 5088518
PMID: 27801290
DOI: 10.1186/s12864-016-3061-z

[…] nstream start codon of each annotated gene.To consider an interaction as positive, an energy threshold of −13 kcal/mol was set as follows. The free energies of the 390 validated interactions from the sRNATarBase 2.0 [] were computed with IntaRNA. A regression was then calculated and plotted between the GC content and the free energy of each interaction. The GC% of M. hyopneumoniae is 28.5 %, of M. […]


Predicting sRNAs and Their Targets in Bacteria

PMCID: 5054197
PMID: 23200137
DOI: 10.1016/j.gpb.2012.09.004

[…] h hybridization energy. Here we assume that only stable seed hybridization results in stable hybridization between two RNA molecules, which was verified by the real sRNA-target mRNA interactions from sRNATarBase .Compared to IntaRNA, sRNATarget and TargetRNA, sTarPicker performed best in both performance of target prediction and accuracy of the predicted binding sites on 17 non-redundant validated […]


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sRNATarBase institution(s)
Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China; Department of Laboratory Medicine, Jinan Military General Hospital, Jinan, China
sRNATarBase funding source(s)
National Key Basic Research and Development Program [2010CB912801]; National Natural Science Foundation of China [31271404, 31071157, 31100960, 31471244, 81572620]

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