<p>You can use <a href="https://github.com/tseemann/barrnap" rel="nofollow noreferrer">Barrnap</a></p>

<pre><code>barrnap -k bac --threads "$(nproc)" \
        -o output_rrna.fna &lt; input_file.fna \
        &gt; output_rrna.gff 2&gt; /dev/null
</code></pre>

<p>Put the file in one line of sequence per fasta id and get sequence with 16S annotation.</p>

<pre><code>perl -pe 'if(/\&gt;/){s/\n/\t/}; s/\n//; s/\&gt;/\n\&gt;/' output_rrna.fa | \
    perl -pe 's/\t/\n/' | tail -n+2 | cut -d\: -f1 | \
    grep -A1 16S &gt; output_16S.fasta
</code></pre>

<p>Check the <code>output_rrna.gff</code> and make a BLAST of the sequence to be sure about the predicted 16S.</p>

CC BY-SA 4.0
2020-02-25T11:30:19.280Z
Thanks zorbax, I am going to have a look and I will give you a comment about what I get
Manolo Dominguez Becerra
CC BY-SA 4.0
2020-02-24T12:18:17.070Z
2020-02-24T12:18:17.070Z
zorbax
<p>You can perform genome annotation using tools like prokka or PGAP. Using some python scripts  you can extract the predicted 16S and blast to confirm.</p>

CC BY-SA 4.0
2021-01-29T23:32:03.450Z
2022-08-11T09:55:37.173Z
2022-08-11T09:55:37.173Z
Kobina
<p>I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output.</p>

<p>Could anyone give me some advice?</p>

CC BY-SA 4.0
2020-02-23T23:32:37.587Z
Have you tried anything any particular? As a general rule, there is no single "best" tool for much of anything, you just need something to give you a reliable result.
Devon Ryan
<genome><bacteria>
Looking for a tool to find 16S rRNA in hundreds of genomes
# Looking for a tool to find 16S rRNA in hundreds of genomes

(Asked by: username_0 on 2020-02-23)

I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output.

Could anyone give me some advice?

**Tags:** genome, bacteria
> **Comments:**
> **username_1**: Have you tried anything any particular? As a general rule, there is no single "best" tool for much of anything, you just need something to give you a reliable result.  

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## 2 answers

### Answer by username_2 on 2020-02-24. Score: 2

You can use Barrnap
barrnap -k bac --threads "$(nproc)" \
        -o output_rrna.fna < input_file.fna \
        > output_rrna.gff 2> /dev/null

Put the file in one line of sequence per fasta id and get sequence with 16S annotation.
perl -pe 'if(/\>/){s/\n/\t/}; s/\n//; s/\>/\n\>/' output_rrna.fa | \
    perl -pe 's/\t/\n/' | tail -n+2 | cut -d\: -f1 | \
    grep -A1 16S > output_16S.fasta

Check the output_rrna.gff and make a BLAST of the sequence to be sure about the predicted 16S.

> **Comments:**
> **username_0**: Thanks zorbax, I am going to have a look and I will give you a comment about what I get  

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### Answer by username_3 on 2021-01-29. Score: 0

You can perform genome annotation using tools like prokka or PGAP. Using some python scripts you can extract the predicted 16S and blast to confirm.


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