How To Identify The 16S Rrna Gene Sequence In A Genome

Question

[Ontheway]

Hi, i have a question about the identification of 16S rRNA gene. One of the common methods is to resequence the 16S rRNA gene and the other is to search the database, such as greengenes. However, if i only have the genome sequence of a bacterial strain and i don't want to resequence the gene, how could i identify the 16S rRNA gene sequence of this strain quickly?

[Neilfws]

"Only" have the genome sequence?!

Answer 1

[cts]

Use RNAmmer either through their web server or by downloading the code and running it locally

Answer 2

[gabriel.jabud]

For people finding this now, there is also Barrnap . Not sure how it compares to RNAmmer but it's super fast and easy to use from a command line.

[suzuBell]

@gabriel.jabud Just wondering, for Barrnap and RNAmmer, is the required input an aligned genome? The barrnap website says "fasta-formatted file with the genome sequence" and RNAmmer website says "full genome sequences". I just wanted to verify, if I had raw read files, this would not be an appropriate input to these programs, right? I would have to align these raw read files first? Thank you.

[colindaven]

It's also worth mentioning Barrnap is in the bacterial annotation system Prokka.

Prokka can be installed on Debian systems with sudo apt install prokka to make your life nice and easy.

Answer 3

[Mensur Dlakic]

There is a long history of identifying "common" non-coding RNAs (tRNA and rRNA) and it can be done very reliably from sequence. In addition to the two excellent suggestions above (RNAmmer and Barrnap), you may want to try SSU-align:

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

This program will not only score small-subunit rRNAs from all three kingdoms, but it will also align them.