I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout for other specimen. So wondering if there is a database with more consistent formatting and such things. I've been looking around BLAST (?), but got confused with the resources, and rather than spinning my wheels, thought I'd ask for some pointers where to start.

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    $\begingroup$ Are you working with annotated genomes? Is there a reason you can’t just pull a .gff file from NCBI? $\endgroup$ – acvill Dec 31 '20 at 2:31
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    $\begingroup$ "I'm interested in finding the start position of each nucleotide in a given genome." Do you mean the start position of each gene? And by "gene", I'm assuming you're restricting it to protein-coding genes? What algorithm will you be using to call genes, as just searching for start codons won't work. $\endgroup$ – MattDMo Dec 31 '20 at 2:43
  • $\begingroup$ @acvill I'm not opposed to any format, just fairly new to this work, and looking for good pointers to start off with; I'll read through the documentation you linked and some examples. Any other resources you might suggest? $\endgroup$ – Chris Dec 31 '20 at 2:47
  • $\begingroup$ @MattDMo "each gene" is just a good place to start, to start working with stuff, as I'm fairly new to this kind of work. For example, on the EcoCyc I link to, it has the position of the start of each gene in the given E coli genome. Are there libraries of the genes in a given genome? $\endgroup$ – Chris Dec 31 '20 at 2:49
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    $\begingroup$ I think @acvill's point is that this work has already been partially or totally completed for quite a number of organisms... $\endgroup$ – MattDMo Dec 31 '20 at 2:49

I would suggest using the FTP at NCBI to download GFF files for whatever organisms you are interested in, as suggested by commenters. GFF files will have annotations for the genome for genes and also for many other features (figure 1).

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Not entirely clear about the goals of this, but if you want annotated coordinates of things in genomes GFFs are a good place to start.

Note that many/most genomes will not have assemblies at the chromosome level, but only at the scaffold/contig level. Depending on your application that may be an issue.

If you want to go to a specific genome/organism, you can search it here. You can access the FTP through the interface for each genome there.


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