Mirna Structure: Searching And Scoring

Question

[Alastair Kerr]

I wish to compare miRNAs based on their predicted secondary (or tertiary) structure and the sequence of the terminal loop. For this I need to implement a system which can:

1. identify related miRNAs
2. align them
3. fold them
4. determine the conservation of the sequence of the terminal loop
5. create a metric that describes the comparison of the two structures

Searching for programs I have found but not yet tested infernal and RSearch the latter looks to be extremely computationally expensive. I am also aware of mfold/unafold.

Any other programs out there? Any heuristics that you can recommend?

Answer 1

[User 3869]

What you want to do seems very similar to miRBase. I thought you could read the following paper before getting start.

The microRNA Registry. Griffiths-Jones S. NAR 2004 32(Database Issue):D109-D111 http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D109

Anyway, you could try ViennaRNA package which is very popular. I applied it on all sequences of miRBase, and it only costed no more than 20 minutes. http://www.tbi.univie.ac.at/~ivo/RNA/