Question: How To Identify The 16S Rrna Gene Sequence In A Genome
0
gravatar for Ontheway
7.3 years ago by
Ontheway10
Ontheway10 wrote:

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?

• 9.8k views
ADD COMMENTlink modified 15 months ago by Mensur Dlakic6.5k • written 7.3 years ago by Ontheway10

"Only" have the genome sequence?!

ADD REPLYlink written 7.3 years ago by Neilfws48k
6
gravatar for cts
7.3 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

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

ADD COMMENTlink written 7.3 years ago by cts1.6k
3
gravatar for gabriel.jabud
15 months ago by
United States
gabriel.jabud40 wrote:

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.

ADD COMMENTlink written 15 months ago by gabriel.jabud40

@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.

ADD REPLYlink written 11 months ago by suzuBell60
1
gravatar for Mensur Dlakic
15 months ago by
Mensur Dlakic6.5k
USA
Mensur Dlakic6.5k wrote:

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.

ADD COMMENTlink written 15 months ago by Mensur Dlakic6.5k
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