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Have a question regarding the game? See if it has been answered here. Frequently asked questions are organized by topic, but it may be helpful to search this page for for a keyword specific to your question.

GeneralEdit

Is EteRNA licensed under free licenses?

EteRNA is free to play. All user content is submitted under the Creative Commons Attribution Non Commercial ShareAlike 3.0 License.


I don't have a strong science background. Will this game be over my head? Will I be any good?

Don't worry! Practically no knowledge of biology or chemistry is required to solve puzzles. As you spend time playing EteRNA, you may find yourself learning quite a bit... and not even realizing it.


Help! I'm stuck on a puzzle! I have no idea what I'm doing!

Hang in there. The EteRNA community is very friendly and eager to help. If you're feeling lost, post a screenshot and ask your question in chat. When you post a screenshot, make sure you enable numbering of nucleotides in your settings. It can make offering help much easier.


How do I take a screenshot?

Click the camera icon on the upper right corner of the chat box. You will be given an option of posting a link to the screenshot in chat. If you simply want to save a picture of a solution, click the link to the picture to open the image in a new browser tab.


Why can't I view my old solutions?

Old solutions have been known to disappear when players log on from different computers or if they delete their flash cookies. Certain browser settings and plugins may also be to blame. Occasionally, your saved solutions may be deleted for no apparent reason. This may indicate that the universe itself hates you. If you have a solution you want to save, take a screenshot.

Puzzle DesignerEdit

Why can't I make a puzzle longer than 400 nucleotides?

The game would take a lot longer to play, and it would likely be less enjoyable. You may notice a lag on larger puzzles. The cost of running an energy minimization increases with sequence length.


Why can't I require more than 1/3 GU pairs?

In the past, there was no limit on the GU restriction. The cap was imposed for a variety of reasons - among which are player enjoyment and relevance to naturally-occurring RNAs.


Can I save a design I'm working on and come back to it later?

Indirectly, yes. Copy the dot-bracket notation of your structure to a notepad file and save. If you have begun placing nucleotides, also save a screenshot. When you want to restart work on your design, input the dot-bracket notation of your design and recreate your original sequence from the screenshot.

Tools and SettingsEdit

Are there hotkeys in EteRNA?

Yes. You can find a list here.


How do I access settings?

Click the gear icon at the bottom of your screen.


What can I do to speed up the game on my computer?

Enabling low performance mode can reduce the demand placed on your computer by the game's graphics. Some amount of lag is unavoidable when solving large puzzles on slower machines.


EnergyEdit

What is free energy and why is it negative?

Main Article: Free Energy
In EteRNA, free energy can be thought of as the energy released into the surroundings when a completely unfolded RNA molecule folds into its shape. A negative sign indicates that energy goes from the RNA into the surroundings when the RNA folds.


Do I need to make free energy as low as possible?

No. When you solve a puzzle, you design a sequence. A sequence can fold into a large number of shapes, each of which have different free energies. The goal of puzzle-solving is to create a sequence whose minimum free energy structure is equivalent to the target structure.


How is energy calculated in EteRNA?


Lab SubmissionsEdit

Does very low or very high free energy ensure a successful design?

No. In nature, RNA does not always adopt its minimum free energy structure. Furthermore, the tools used to predict the minimum free energy structure are imperfect.


What is the optimal free energy?

No specific value of free energy is ideal. Most successful lab designs do not attempt achieve the maximum or minimum value of free energy possible for a given secondary structure.


Why shouldn't I use all GC pairs in a lab design?

GC-rich sequences are difficult to synthesize and prone to being caught in folding traps. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.


Why shouldn't I use all AU or GU pairs in a lab design?

AU and GU pairs are weaker than GC pairs. Alone, they are unlikely to hold an RNA molecule in a specific structure. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.


What is the optimal balance of AU, GU, and GC-pairs?

In general, designs with ~60% GC pairs tend to balance stability and ease of synthesis. This rule is not absolute, however. The frequency of GC pairs in some winning lab designs has exceded 70%.

Dotplots and Melt PlotsEdit

What is a "melting plot" and does it mean to "melt" RNA?

As temperature increases, base pairs are broken. In EteRNA, the melting temperature can be thought of as the temperature at which there would be enough energy to pull the structure apart from its folded structure to a linear form. The process of increasing temperature to break base pairs and create a completely unpaired strand of RNA is called "melting". In EteRNA, the melt plot shows the percentage of unpaired bases as a function of temperature.


How can I view the melting plot or dot plot?

Click the eye icon at the bottom of the screen while designing a lab submission.


What does a dotplot show?

A dotplot shows the probability of any two bases forming a base pair.


How do I read a dotplot?

The x and y axes of a dotplot represent individual nucleotides in the RNA molecule. Points within the dotplot represent interactions between bases. The point 4, 20 and the point 20, 4 both refer to the interaction between bases 4 and 20. A dotplot is divided diagonally into two triangles. The bottom left triangle shows only the base pairs present in the minimum free energy structure. The top right triangle shows the predicted probability of base pairs forming in nature. The darker the square in the top right triangle, the greater the probability of that base pair forming.

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