<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>

CC BY-SA 3.0
2017-07-19T08:31:11.713Z
2017-07-19T08:31:11.713Z
AudileF
<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>

<fasta><gff3><sequence-analysis>
Does Prokka or gff3 change the sequence / subject ID of fasta files?
# 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

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## 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.


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