How to convert a DNA alignment to RNA (T to U)?

Hi, I have RNA alignments for several viral genes from an RNA virus, the problem is that genbank stores the RNA genome as DNA (T’s not U)… And thus if I run the RNAalignfold webservice, I generate the structure but I have no way to view the structure with Varna. Other than editing in a text editor before import, is there any way to convert an alignment to RNA within Jalview ?

regards, Keith

The problem is also that even if I convert the DNA to RNA (T → U) in the fasta alignment before importing to Jalview, when I run the RNAsecondary structure prediction (Vienna package, RNAalignfold), I get the dot bracket secondary structure, but no popup menu option to see the structure in Varna (like what you get when you load an RFAM alignment…). I’m confused as to how to get Jalview to treat the alignment as RNA…



We’ve been working on fixing some of these issues in the upcoming Jalview 2.11.3 release - though I see just now that the RNAAliFold output is not being recognised as importable to VARNA - which is definitely a bug we need to fix.

Have a go with the latest Jalview Test installation and see how far you can get: - this at least fixes the DNA/RNA import issue, but for RNAAliFold, you may need to export the secondary structure annotation as a Jalview annotation file, remove the ‘.’'s and import again.

Hi, ok the new version works once the ‘.’ are removed from the saved annotation file and re-imported to the alignment! Thanks for the quick response! Now I need to learn how Varna works in detail to only visualise parts of the large alignment (it turns it into a large spaghetti)! Keith

I looked at this a little more: a quick workaround with the RNAliFold issue is to export the annotated alignment as Stockholm, then change ‘MFE_Structure’ to ‘SS’ and hit the ‘Open’ button to import. Of course it would be easier if we just fixed it - but we might not manage before our first release of 2.11.3 (hit the ‘watch issue’ button on if you want to be notified when we get a patch).

Once you have the annotion imported the right way, you can focus on just parts of the structure by just deleting the regions either side - again not at all perfect. I’ve reported the ability to more easily filter what Jalview displays in VARNA as an issue here: