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Publications for sRNATarBase
Global Screening of Salmonella enterica Serovar Typhimurium Genes for Desiccation Survival
[…] 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
[…] 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
[…] 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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