2D Rna Structure For Proteins.

Question

[Hanan]

Hi everyone

I have two datasets of proteins, Secreted and cytoplasmic.Each set includes at least 10 genes. I get their RNA cods and I want to look at their structures to figure out whether there are any similarity shape or pattern in each sets or maybe what is the major difference between them !!

I did the following:

1. I'm interesting only in first 12 codons, so I cut the sequences to 12 letters only.
2. I used MATLAB to get their DNA sequences and then their RNA sequences from its DNA cods.
3. I have plotted their 2D structure by MATLAB using following cods:

seq = rna(1:36); ss = rnafold(seq); rnaplot(ss, 'sequence', seq, 'format', 'diagram');

the results was very tricky. By looking at their structures, I could not realize what is the common differences or similarities between them !!

I'm thinking now if there is any statical analysis that shows some quantitative measurement? And Does this measuring, for example like: Variance, level of variation, similarity score) will describe their 2d RNA structures ? If so, which tool I have to use ?

Is my way of thinking wrong ?

I did local alignment between seq in each class, and it shows some similarities region between the beginning of seq. and middle seq. as well.

Any suggestion to reach my goal?

Sorry for my poor language and Thanks in advance ..

Nana

Answer 1

[Asaf]

There are several approaches you can take.
Since you have a multiple alignment already you can calculate its consensus secondary structure if it exists using RNAalifold of the Vienna package. If you'll get a structure it's a good sign, you can then try and look for conserved small structures and sequences and maybe figure out their role (template for protein binding etc.)
Another approach is to try and find a common motif in all the RNA structures, this can be done with a tool from Eran Segal's lab for instance.
Good luck