Tips and Tricks: Difference between revisions
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<li><span style="font-family: helvetica;">[[Boosting]] can help lower loop energy.<br /></span></li> | <li><span style="font-family: helvetica;">[[Boosting]] can help lower loop energy.<br /></span></li> | ||
<li><span style="font-family: helvetica;">Using [[special sequences]] may be required to create certain secondary structures.</span></li> | <li><span style="font-family: helvetica;">Using [[special sequences]] may be required to create certain secondary structures.</span></li> | ||
<li><span style="font-family: helvetica;">[[Exchanging the positions of two paired bases]] can often stabilize long stacks that have mispaired.</span></li> | <li><span style="font-family: helvetica;">[[Base Pair Flipping|Exchanging the positions of two paired bases]] can often stabilize long stacks that have mispaired.</span></li> | ||
<li><span style="font-family: helvetica;">[[Blocking]] can prevent the formation of undesired base pairs.</span></li> | <li><span style="font-family: helvetica;">[[Blocking]] can prevent the formation of undesired base pairs.</span></li> | ||
<li><span style="font-family: helvetica;">[[Deliberately destabilizing unwanted structures]] may be necessary to prevent the formation of undesired loops.</span></li> | <li><span style="font-family: helvetica;">[[Hidden Instabilities|Deliberately destabilizing unwanted structures]] may be necessary to prevent the formation of undesired loops.</span></li> | ||
</ul> | </ul> | ||
<p> </p> | <p> </p> | ||
<h3><span style="font-family: helvetica;">Labs</span></h3> | <h3><span style="font-family: helvetica;">Labs</span></h3> | ||
<ul> | <ul> | ||
<li><span style="font-family: helvetica;">Avoid submitting designs with excess [[AU]], [[GU]], or [[GC]] pairs!</span></li> | <li><span style="font-family: helvetica;">Avoid submitting designs with excess [[AU Pair|AU]], [[GU Pair|GU]], or [[GC Pair|GC]] pairs!</span></li> | ||
<li><span style="font-family: helvetica;">Leave all loops as adenine, unless you wish to [[boost]] your design. Boosting may or may not be helpful in lab.</span></li> | <li><span style="font-family: helvetica;">Leave all loops as adenine, unless you wish to [[Boosting|boost]] your design. Boosting may or may not be helpful in lab.</span></li> | ||
<li><span style="font-family: helvetica;">[[Use of secondary structure prediction programs]] can identify very poor designs, but these programs are of uncertain value in determining which of two reasonable designs is superior.</span></li> | <li><span style="font-family: helvetica;">[[Use of secondary structure prediction programs]] can identify very poor designs, but these programs are of uncertain value in determining which of two reasonable designs is superior.</span></li> | ||
<li><span style="font-family: helvetica;">[[Even Energy Distribution]] is a hypothesis that stabilizing or destabilizing features should not be concentrated in one area of a lab design.</span></li> | <li><span style="font-family: helvetica;">[[Even Energy Distribution]] is a hypothesis that stabilizing or destabilizing features should not be concentrated in one area of a lab design.</span></li> | ||
<li><span style="font-family: helvetica;">[[Copying elements from previously successful designs]] has been moderately effective.</span></li> | <li><span style="font-family: helvetica;">[[Copying elements from previously successful designs]] has been moderately effective.</span></li> | ||
</ul> | </ul> | ||
Revision as of 12:12, 17 April 2013
Puzzles and lab differ considerably in EteRNA. Tactics and strategies that are effective in one aspect of the game are not guaranteed to help in others.
Puzzles
Puzzles in EteRNA vary widely in difficulty. Many solutions can be found quickly, without using every tactic available. The hardest puzzles often employ creative uses of the "rules" that dictate how RNA folds in EteRNA.
- Creating a good starting sequence can help you solve easy puzzles more quickly.
- Placing GC pairs at the end of stacks is often an effective way of lowering energy.
- Boosting can help lower loop energy.
- Using special sequences may be required to create certain secondary structures.
- Exchanging the positions of two paired bases can often stabilize long stacks that have mispaired.
- Blocking can prevent the formation of undesired base pairs.
- Deliberately destabilizing unwanted structures may be necessary to prevent the formation of undesired loops.
Labs
- Avoid submitting designs with excess AU, GU, or GC pairs!
- Leave all loops as adenine, unless you wish to boost your design. Boosting may or may not be helpful in lab.
- Use of secondary structure prediction programs can identify very poor designs, but these programs are of uncertain value in determining which of two reasonable designs is superior.
- Even Energy Distribution is a hypothesis that stabilizing or destabilizing features should not be concentrated in one area of a lab design.
- Copying elements from previously successful designs has been moderately effective.
