How to download an assembly using accession number in GFF3 format from NCBI?

Question

[nazukbedi007]

Hello, I want to download an assembly for an E.coli genome with the accession number: GCF_000005855.1 in GFF3 format. However, I am not able to find a download assembly option on this page. Link to the NCBI page with the assembly

There is an updated version of this assembly as well, and the NCBI page for the updated assembly does have a download assembly option. Link to the NCBI page of the updated assembly

I am unsure about how to download the GFF3 file for the older assembly, whose accession number I have mentioned above. Could somebody kindly help me with this? Thank you very much.

[GenoMax]

Assemblies are not in GFF3 format. Annotations for the assemblies use that format. Do you want to download an older versions of assembly (i.e sequence) along with the GFF3 file?

It looks like NCBI does not make the older assembly data available any longer: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.1_ASM584v1/

[nazukbedi007]

Yes I meant the annotations for the assembly in the GFF3 file with the sequence information, sorry about that.

Do you know if there is any other way to get GFF3 file for the older version, if it's not available at the ncbi link? Thank you!

[GenoMax]

That may be tough unless you can find an archival copy from some place.

Answer 1

[Sej Modha]

You could download the GFF3 from https://www.ncbi.nlm.nih.gov/nuccore/U00096.2 associated with the previous assembly version (https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.1/#/def).

Go to https://www.ncbi.nlm.nih.gov/nuccore/U00096.2 and then click on Send to -> File -> Format -> GFF3 for the older version of GFF.

[nazukbedi007]

This is what I needed, thank you so much!!