[DIYbio] Re: Any use for RNA secondary structure prediction? (slash help getting started?)

Probably there are tons of things that are important for RNA folding.

-The 5'UTR of CDS determine translation initiation efficiency (heavy secondary structures may keep the ribosomes from binding)
- crispr: maybe you can engineer the scaffold (change certain bases that are non essential, to keep homologous recombination from occuring in multiplex constructs)
-crispr2: maybe it is possible to express the guide (19-20 bp that tells where to cut in the genome) and the scaffold (80 bp, that binds to cas9 enzyme) seperately and then join them by some weird RNA mechanism. It is a pain in the *** to express 10 guides, because you would need the scaffold 10 times. Costing synthesis (especially repeats are difficult and $$$)


On Monday, August 10, 2015 at 11:37:16 PM UTC+2, Michael Flynn wrote:

Hi all,

I recently wrote my undergraduate thesis on RNA secondary structure prediction algorithms. In the process I've become intimately familiar with the algorithms and code bases behind Unafold and RNAstructure, which I have been told comprise 90% of the market share of RNA structure prediction software. My thesis is located here, if you are interested.  

However, I was a physics and computer science student, and I have minimal (no) training in biology. This meant that most of the time while I was writing my thesis I was in great want of background knowledge and motivation. I was often asked why my research was important, but I could never give a strong answer. When I asked my advisor for motivations behind our work, he did not answer to my satisfaction. So I thought, what better way to learn than DIYbio?

So are there ways I could help this community? What would be the best path for me to get started, in a way that my background would be the most relevant? 

Mike