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!
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Timotheus •
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.
Thank you Mensur Dlakic, apologies for a late reply. The tools look interesting, I'll try to give them a try!
Additionally, you can search against the SILVA database.
Probably the easiest way is to use MOSGA, that can use barrnap and SILVA.
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