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.

  • $\begingroup$ LoL, sure, but I don't what all genes, only blaZ for example. $\endgroup$
    – Soerendip
    Dec 8, 2020 at 19:01
  • $\begingroup$ I found Piggy. academic.oup.com/gigascience/article/7/4/giy015/4919733 $\endgroup$
    – Soerendip
    Dec 8, 2020 at 19:02
  • 1
    $\begingroup$ Get a GTF/bed file of the gene coordinates and use bedtools perhaps $\endgroup$ Dec 8, 2020 at 19:09
  • $\begingroup$ 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? $\endgroup$
    – Jesse
    Dec 9, 2020 at 16:59
  • $\begingroup$ 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. $\endgroup$
    – Soerendip
    Dec 9, 2020 at 17:37


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