Tools for rRNA gene annotations

Question

[Timotheus]

Hello, I have a metazoan contig that I suspect to contain rRNA genes. Would you be able to recommend software designed to predict rRNA genes? I'd be grateful for suggestions!

Answer 1

[Mensur Dlakic]

If you want to know quickly, barrnap may do the trick:

https://github.com/tseemann/barrnap

For maximum sensitivity, I suggest ssu-align:

http://eddylab.org/software/ssu-align/

I am tempted to engage in discussion whether rRNA is really a gene, though I understand historic precedent for calling it so. Instead, I will just point out that there is a difference between coding and non-coding RNA.

[Timotheus]

Thank you Mensur Dlakic, apologies for a late reply. The tools look interesting, I'll try to give them a try!

[BioinformaticBird]

Additionally, you can search against the SILVA database.

Answer 2

[BioinformaticBird]

Probably the easiest way is to use MOSGA, that can use barrnap and SILVA.