| Chapter title |
Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm
|
|---|---|
| Chapter number | 15 |
| Book title |
RNA Structure Determination
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-6433-8_15 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6431-4, 978-1-4939-6433-8
|
| Authors |
Paul Dallaire, François Major |
| Abstract |
We created an accelerated version of MC-Fold called MC-Flashfold that allows us to compute large numbers of competing secondary structures including noncanonical base pairs. We visualize the base pairs in these sets using high quality intuitive dot plots and arc plots. Our new tools allow us to explore RNA dynamics by visualizing the competing structures in free energy bands. Here we describe how to use these tools to generate dot plots that reveal the postulated anti-terminator stem in the E. coli trp operon leader sequence. These plots show the anti-terminator hairpin loop during transcription and as a minor population of the full-length leader sequence. This is a case of switching RNA structure that had been originally postulated based on short dyad inverted repeats. Other switching RNA sequences can be analyzed by using our method. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 11 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 3 | 27% |
| Student > Master | 2 | 18% |
| Professor | 1 | 9% |
| Student > Bachelor | 1 | 9% |
| Researcher | 1 | 9% |
| Other | 1 | 9% |
| Unknown | 2 | 18% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 45% |
| Agricultural and Biological Sciences | 2 | 18% |
| Physics and Astronomy | 1 | 9% |
| Chemistry | 1 | 9% |
| Unknown | 2 | 18% |