<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>

CC BY-SA 4.0
2020-12-08T19:01:28.237Z
LoL, sure, but I don't what all genes, only blaZ for example.
Soerendip
CC BY-SA 4.0
2020-12-08T19:02:03.200Z
I found Piggy. https://academic.oup.com/gigascience/article/7/4/giy015/4919733
Soerendip
CC BY-SA 4.0
2020-12-08T19:09:38.823Z
Get a GTF/bed file of the gene coordinates and use bedtools perhaps
Chris_Rands
CC BY-SA 4.0
2020-12-09T16:59:02.133Z
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?
Jesse
CC BY-SA 4.0
2020-12-09T17:37:54.723Z
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.
Soerendip
CC BY-SA 4.0
2020-12-09T22:43:27.260Z
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.)
Jesse
<genome><genomics><microbial-genomics>
How to extract certain genes including non-coding regions?
# 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

