Rna Structure Similarity Search

Question

[Nicolas Rosewick]

Hi,

To analyze newly discovered transcript (like lncRNAs), I want to check if the structure of interesting RNA candidates are similar to known RNAs, and to have maybe an idea of their function. Anyone has an idea to to such a thing ?

Thanks

N.

Answer 1

[Asaf]

You might want to use Infernal to screen the new RNAs with the entire Rfam library (use cmscan command), you can download the Rfam models from the Infernal website and easily scan the RNA sequences you found to see if they match the model, which integrates structure and sequence, of a known RNA family

Answer 2

[Johanna Schott]

If you are talking about only one or a few transcripts, you can manually compare your newly discovered structure to already described families of RNA structures.

The following paper describes conserved families of RNA structures:

Parker, B.J., Moltke, I., Roth, A., Washietl, S., Wen, J., Kellis, M., Breaker, R., and Pedersen, J.S. (2011). New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res. 21, 1929–1943.

Here you find links that lead you to the described RNA structures in the UCSC Genome browser:

http://moma.ki.au.dk/prj/mammals/

[Nicolas Rosewick]

Yes I have only a few transcripts to check. I checked in RFAM (sequence search) but nothing comes out. So my idea is to download all the known lncRNA and to check for sequence similarity. Is Infernal (like Asaf recommend me) a good options to do such a thing ?

[Johanna Schott]

I don't have any experience with Infernal and can't give you advice on that. I rather thought of using predicted structures of lincRNAs in the EvoFold table of the UCSC Genome browser. This prediction is based on conservation between species. The paper that I mentioned groups predicted structures into families. You could download all structures that were predicted for lincRNAs in the Evofold track and compare them programmatically to structures that are potentially contained in your lincRNA. Or you have a look at the families described in the paper, because some of them are lincRNAs (e.g. the Malat1 family). You could also use EvoFold (the program that was used to create the EvoFold table) and apply it yourself to an alignment of several species in the region of the genome where your lincRNA comes from. Provided your lincRNA (and parts of its structure) are conserved between species, you might find something interesting that way.

[Asaf]

The Rfam search uses infernal (After a preliminary Blast search) so I wouldn't bother to run infernal again