Tools for recovering ribosomal RNA sequences from whole genome assemblies
1
0
Entering edit mode
13 months ago
ddh8602 • 0

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.

ribosomal genome Assembly • 489 views
ADD COMMENT
0
Entering edit mode

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)

ADD REPLY
2
Entering edit mode
13 months ago
Mensur Dlakic ★ 15k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1946 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6