Answers.Body: <p>Prokka is an annotation tool. It takes your contigs file with fasta headers <code>&gt;NODE_108...</code>and searchs for ORFs and their putative functions. Prokka produces submission ready output, the new fasta headers you see <code>&gt;JHIOGLGG_28...</code>are locus tags and gene description from the annotation and are not related to contig node data. Please see the <a href="https://github.com/tseemann/prokka#output-files" rel="nofollow noreferrer">github information page</a> for more info.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-19T08:31:11.713Z
Answers.LastActivityDate: 2017-07-19T08:31:11.713Z
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Body: <p>I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match the sequence id's of the fasta files. The files I just produced with prokka have a different seqid than my fasta files. My fasta files look like this </p>
  
  <pre><code>&gt;NODE_108_length_645_cov_0.679537_ID_215
  </code></pre>
  
  <p>However the prokka output gff3 file for the same fasta file uses a seqid like this</p>
  
  <pre><code>gnl|X|JHIOGLGG_28
  </code></pre>
  
  <p>What would cause this difference? And do the last digits still correlate to the same seqid's even though the string before it has changed?</p>
  
Tags: <fasta><gff3><sequence-analysis>
Title: Does Prokka or gff3 change the sequence / subject ID of fasta files?
ThreadText: # Does Prokka or gff3 change the sequence / subject ID of fasta files?
  
  (Asked by: username_0 on 2017-07-18)
  
  I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match the sequence id's of the fasta files. The files I just produced with prokka have a different seqid than my fasta files. My fasta files look like this
  
  ```
  >NODE_108_length_645_cov_0.679537_ID_215
  
  ```
  
  However the prokka output gff3 file for the same fasta file uses a seqid like this
  
  ```
  gnl|X|JHIOGLGG_28
  
  ```
  
  What would cause this difference? And do the last digits still correlate to the same seqid's even though the string before it has changed?
  
  **Tags:** fasta, gff3, sequence-analysis
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-07-19. Score: 3 | Accepted answer
  
  Prokka is an annotation tool. It takes your contigs file with fasta headers `>NODE_108...`and searchs for ORFs and their putative functions. Prokka produces submission ready output, the new fasta headers you see `>JHIOGLGG_28...`are locus tags and gene description from the annotation and are not related to contig node data. Please see the [github information page](https://github.com/tseemann/prokka#output-files) for more info.
  
  
  ---
  
  