Tools for recovering ribosomal RNA sequences from whole genome assemblies

Question

[ddh8602]

Hi everyone! I am searching for a tool to recover ribosomal RNA sequences from a bunch of whole genome assemblies I have (Listeria sp.) for phylogeny purposes. Some important points: I only have the assemblies not the raw data and preferably not online tools as I have around 150 genomes. Until now I have found Anvio-6.2 (anvi-get-sequences-for-hmm-hits) and SortMeRNA, but both are focused on metagenomic reads, not sure if this can affect my results. I appreciate your suggestions.

[lieven.sterck]

since you're talking about genome assemblies I assume you will also mean rDNA regions? (if not I would be quite surprised to see rRNA mixed in you DNA samples)

There are tools around to identify those rDNA regions (well they actually screen for the resulting rRNAs)

Answer 1

[Mensur Dlakic]

SSU-ALIGN is most thorough but slow, and works only for 16S rRNA. RNAmmer has a server but can also be downloaded. Finally, you may want to try barrnap.

[ddh8602]

Thanks Mensur, I ended up using RNAmmer, great tool and precise.