Body: <p>I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with <code>Roary</code>. However, we are also interested in comparing non-coding regions. Is there a tool that can do that or a tool that tells me what region in the full assembly is relevant? The assembly and extracted genes are present as <code>fasta</code> and <code>fa.ali</code> (alignment) files. The genomes are from bacteria.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-08T19:01:28.237Z
Comments.Text: LoL, sure, but I don't what all genes, only blaZ for example.
Comments.UserDisplayName: Soerendip
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-08T19:02:03.200Z
Comments.Text: I found Piggy. https://academic.oup.com/gigascience/article/7/4/giy015/4919733
Comments.UserDisplayName: Soerendip
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-08T19:09:38.823Z
Comments.Text: Get a GTF/bed file of the gene coordinates and use bedtools perhaps
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-09T16:59:02.133Z
Comments.Text: Can you give more information about what you did with Roary?  I'm not familiar with it, but the docs say it takes GFF3 as input, so could your input files already have what you need?
Comments.UserDisplayName: Jesse
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-09T17:37:54.723Z
Comments.Text: Roary is a pan-genome tool. I processed full genome assemblies first with Prokka which generates GFF3 files and then with Roary to get a gene presence/absence map. Yes, Roary uses GFF3 files, which probably are indexed. That is a good point. Is there a tool though that can extract certain genes from GFF3 files? Including non-coding part.
Comments.UserDisplayName: Soerendip
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-09T22:43:27.260Z
Comments.Text: I don't know enough about what existing tools are out there that might do it for you without extra coding, but the format is really just tab-separated text, so at the very least you can read them as spreadsheets and see what the feature column looks like.  For example in some GFF3 files I have from NCBI I see things like region, gene, mRNA, exon, and CDS, each with associated start and end positions.  So you could take the region for, say, "gene," to get both coding and non-coding parts.  (Depends on what's in your files, though!  Maybe share a few lines as an example.)
Comments.UserDisplayName: Jesse
Tags: <genome><genomics><microbial-genomics>
Title: How to extract certain genes including non-coding regions?
ThreadText: # How to extract certain genes including non-coding regions?
  
  (Asked by: username_0 on 2020-12-08)
  
  I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with `Roary`. However, we are also interested in comparing non-coding regions. Is there a tool that can do that or a tool that tells me what region in the full assembly is relevant? The assembly and extracted genes are present as `fasta` and `fa.ali` (alignment) files. The genomes are from bacteria.
  
  **Tags:** genome, genomics, microbial-genomics
  
  > **Comments:**
  > **username_0**: LoL, sure, but I don't what all genes, only blaZ for example.  
  > **username_0**: I found Piggy. https://academic.oup.com/gigascience/article/7/4/giy015/4919733  
  > **username_1**: Get a GTF/bed file of the gene coordinates and use bedtools perhaps  
  > **username_2**: Can you give more information about what you did with Roary?  I'm not familiar with it, but the docs say it takes GFF3 as input, so could your input files already have what you need?  
  > **username_0**: Roary is a pan-genome tool. I processed full genome assemblies first with Prokka which generates GFF3 files and then with Roary to get a gene presence/absence map. Yes, Roary uses GFF3 files, which probably are indexed. That is a good point. Is there a tool though that can extract certain genes from GFF3 files? Including non-coding part.  
  > **username_2**: I don't know enough about what existing tools are out there that might do it for you without extra coding, but the format is really just tab-separated text, so at the very least you can read them as spreadsheets and see what the feature column looks like.  For example in some GFF3 files I have from NCBI I see things like region, gene, mRNA, exon, and CDS, each with associated start and end positions.  So you could take the region for, say, "gene," to get both coding and non-coding parts.  (Depends on what's in your files, though!  Maybe share a few lines as an example.)  
  
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  ## 0 answers
  
  