Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-25T11:30:19.280Z
Answers.Text: Thanks zorbax, I am going to have a look and I will give you a comment about what I get
Answers.UserDisplayName: Manolo Dominguez Becerra
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-24T12:18:17.070Z
Answers.LastActivityDate: 2020-02-24T12:18:17.070Z
Answers.UserDisplayName: zorbax
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-29T23:32:03.450Z
Answers.LastActivityDate: 2022-08-11T09:55:37.173Z
Answers.LastEditDate: 2022-08-11T09:55:37.173Z
Answers.UserDisplayName: Kobina
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-23T23:32:37.587Z
Comments.Text: 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.
Comments.UserDisplayName: Devon Ryan
Tags: <genome><bacteria>
Title: Looking for a tool to find 16S rRNA in hundreds of genomes
ThreadText: # 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.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-02-24. Score: 2
  
  You can use [Barrnap](https://github.com/tseemann/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 username_2, I am going to have a look and I will give you a comment about what I get  
  
  ---
  
  ### 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.
  
  
  ---
  
  