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| Content Provider | PubMed Central |
|---|---|
| Author | Amman, Fabian Flamm, Christoph Hofacker, Ivo |
| Copyright Year | 2012 |
| Abstract | Bacterial small non-coding RNA (sRNA) plays an important role in post-transcriptional gene regulation. Although the number of annotated sRNA is steadily increasing, their functional characterization is still lagging behind. Various computational strategies for finding sRNA–mRNA interactions, and thus putative sRNA targets, were developed. Most of them suffer from a high false positive rate. Here, we present a qualitative model to simulate the effect of an sRNA on the translation initiation of a potential target. Information about the ribosome–mRNA interaction, sRNA–mRNA interaction and expression information from deep sequencing experiments is integrated to calculate the change in translation initiation complex formation, as a proxy for translational activity. This model can be used to post-evaluate predicted targets, hence condensing the list of potential targets. We show that our translation initiation model, under the influence of an sRNA, can successfully simulate thirteen out of fifteen tested sRNA–mRNA interactions in a qualitative manner. To show the gain in specificity, we applied our method to a target search for the Escherichia coli sRNA RyhB. Compared with simple target prediction without post-evaluation, we reduce the number of targets to less than one fourth potential targets, considerably reducing the burden of experimental validation. |
| Related Links | http://dx.doi.org/10.3390/ijms131216223 |
| Ending Page | 16240 |
| Page Count | 18 |
| Starting Page | 16223 |
| File Format | |
| ISSN | 14220067 |
| e-ISSN | 14220067 |
| Journal | International Journal of Molecular Sciences |
| Issue Number | 12 |
| Volume Number | 13 |
| Language | English |
| Publisher | Molecular Diversity Preservation International (MDPI) |
| Publisher Date | 2012-11-01 |
| Access Restriction | Open |
| Rights Holder | Molecular Diversity Preservation International (MDPI) |
| Subject Keyword | Physical and Theoretical Chemistry Inorganic Chemistry Organic Chemistry Spectroscopy Molecular Biology Catalysis Computer Science Applications Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Spectroscopy Organic Chemistry Medicine Molecular Biology Physical and Theoretical Chemistry Catalysis Inorganic Chemistry Computer Science Applications |
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