Interpreting the output of an mRNA structural motif search algorithm

Question

[Joel Wallenius]

Hello!

I am searching for motifs in some hundreds of mRNA sequences. I couldn't find any, so now I'm searching for structural motifs instead. I am not familiar with any such software so I just used the first one that worked without hassle - 'RNAProfile'.

Its output includes some patterns like (((.((.(((....))))))))) plus some numbers 'E' and 'Fitness'.

Does anybody here have experience with interpretation of this type of output? I don't have anything to calibrate with, so can't tell if there's anything significant in the results :/

Big thanks in advance!

Answer 1

[Martombo]

The profile you see, with brackets and dots, indicates whether a nucleotide is paired in the secondary structure (open bracket goes with the corresponding closed one) or unpaired (a dot). For example:

AAAAAAAAANNNNNNNUUUUUUUUU
(((((((((.......)))))))))

You can use RNAfold web server to clarify this. You can read up the definition they use for fitness and energy (E) in their paper.

To compute the significance of the energy or the presence of a motif you can compare it to the results of scrambled sequences.