Hi Fellow Eterna Players,
I finally released Serena as a Pypi package that is pip installable with python via the command “pip install serena-rna-tool”. You can find the website for it here along with link to documentation and the github for it.
https://pypi.org/project/serena-rna-tool/
This software package has all the tools I presented at Eternacon9 as well as some other stuff I have been working on. It features a framework that is designed to hold and shuttle around the secondary strucutures of the ensemble in a way that makes them easily accessable for automation around them. You can read more about it at the project homepage from the pypi repo webpage. There are also some simple api’s around Nupack4 and Vienna2 for mfe and subopt folding.
Currently Serena generates data that looks like this.
You can see that the highest fold change equates to a middline Serena score and the highest and lowest score are for the lowest fold change. This I belive is because the excessive low score are for excessive secondary structures as well as too many negative properties of a switch. The super high score are due to an excessive amount of features that are indicative of a switch and no penatlies, so much to the point I think it is too unstable to keep its unbound shape and thus switch properly. From the conferenece we heard from researchers who pointed out how sensitive RNA switches are and I think this is bore out in the plots. A really good switch should have as little variation as possible but still have some properties of a good switch and have some echo of the bound state. I belive that this further points to static stems being important and I belive that a static stem detector may be the next step needed. If you want to help with the project let me know. You can also create an issue in github, create a fork, and then send me a PR for any changes you think should be made.
Respectfully,
Jennifer