Body: <p>I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, but I'm only interested in one for now) was tagged as 'investigate' in the QC column of the gene_presence_absence matrix, so I did some investigating. Looking at this sequence, I saw it was a hypothetical protein of around 4k bases, and when I ran it through BLAST on the NCBI website, far from being unique, it gave 100% matches to many other L. plantarum strains. Further investigation suggests that this sequence was present on a contig not much larger than the 'gene' its self.</p>
  <p>I have two questions.</p>
  <ol>
  <li><p>any ideas why this was identified as unique by Roary but ubiquitous in other members of the species on BLAST (accepting that it's possible it genuinely is unique among my 30 or so strains, but common in the species more generally - it just seems unlikely) - maybe something to do with poorly called open reading frame in prodigal (genome was annotated by prokka)? Or something to do with Roary separating paralogs?</p>
  </li>
  <li><p>what is the simplest way of confirming if this 4k sequence is/isn't present in my group of 30 genomes?</p>
  </li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-02T10:20:52.607Z
Comments.Text: Any reason you don't just BLASTn your sequence against your 30 genomes to check?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-02T11:50:44.870Z
Comments.Text: That was my thinking. Would I just use the assemblies to make a blast database and then blast against my 'gene'?
Comments.UserDisplayName: Mark
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-02T11:52:42.727Z
Comments.Text: You'd blast your gene against the database, but yes. That will immediately show you if the sequence is indeed unique or not. Then you can focus on the first question.
Comments.UserDisplayName: terdon
Tags: <genome><bacteria><sequence-annotation>
Title: Search for specific sequence in group of bacterial genomes
ThreadText: # Search for specific sequence in group of bacterial genomes
  
  (Asked by: username_0 on 2021-07-01)
  
  I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, but I'm only interested in one for now) was tagged as 'investigate' in the QC column of the gene\_presence\_absence matrix, so I did some investigating. Looking at this sequence, I saw it was a hypothetical protein of around 4k bases, and when I ran it through BLAST on the NCBI website, far from being unique, it gave 100% matches to many other L. plantarum strains. Further investigation suggests that this sequence was present on a contig not much larger than the 'gene' its self.
  
  I have two questions.
  
  1. any ideas why this was identified as unique by Roary but ubiquitous in other members of the species on BLAST (accepting that it's possible it genuinely is unique among my 30 or so strains, but common in the species more generally - it just seems unlikely) - maybe something to do with poorly called open reading frame in prodigal (genome was annotated by prokka)? Or something to do with Roary separating paralogs?
  2. what is the simplest way of confirming if this 4k sequence is/isn't present in my group of 30 genomes?
  
  **Tags:** genome, bacteria, sequence-annotation
  
  > **Comments:**
  > **username_1**: Any reason you don't just BLASTn your sequence against your 30 genomes to check?  
  > **username_0**: That was my thinking. Would I just use the assemblies to make a blast database and then blast against my 'gene'?  
  > **username_1**: You'd blast your gene against the database, but yes. That will immediately show you if the sequence is indeed unique or not. Then you can focus on the first question.  
  
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  ## 0 answers
  
  