User:ElNando888/Self-interacting sequences: Difference between revisions
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<td>MFE<br />(Vienna 2.1.1) </td> | <td>MFE<br />(Vienna 2.1.1) </td> | ||
<td><code>.......(((((...(((((.((..(.((((.((.....)))))))..)).))))))))))..</code></td> | <td><code>{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}</code></td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>Constrained folding</td> | <td>Constrained folding</td> | ||
<td><code>.......(((((..((((......))))((..((((((......))))))..))..)))))..</code></td> | <td><code>{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}</code></td> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
Revision as of 14:35, 22 May 2013
(work in progress)
== The idea ==
In the future, EteRNA players will face the challenge of creating RNA sequences that can change shape by binding other RNAs rather than reacting to ligands like FMN or Theophylline.
A well-known interaction HIV TAR-TAR*
PDB accession 1KIS.
== Parameters for candidates ==
"Natural" folding (MFE) should
- not have the hairpin features
- not have the complementary sequences bound
Constrained folding should
- have the hairpin features
- have as few free bases as possible in the portion inbetween (in an attempt to guarantee that the stems will coaxially stack, thereby nullifying risks of pseudoknot formation)
== Examples ==
=== Candidate 1 ===
<tbody> </tbody>| Sequence | AAACAGUUGGCUUGAGCCCUGGGAGGCUCUGAGGCUGUUCCCAGACAGCUGAGGGUGGCCAUC |
| MFE (Vienna 2.1.1) |
.......(((((...(((((.((..(.((((.((.....)))))))..)).)))))))))).. |
| Constrained folding | .......(((((..((((......))))((..((((((......))))))..))..))))).. |
