Question: How can I figure out the NCBI annotation version of a GFF file?
gravatar for colin.kern
6 months ago by
United States
colin.kern200 wrote:

I am writing a manuscript for a study that used the NCBI annotations for the chicken, cattle, and pig genomes. The analysis was performed over a year ago using the current annotations for those species, however they have all been updated on NCBI since. As far as I can tell the annotation release version is not indicated in these files, so I'm having trouble determining the versions for these annotations. I can't find a way to look at older versions of annotations or even a timetable of what version was released when so I can match the approximate date of download to the version that was current at that time. Is there any way I can find the versions of these annotations?

rna-seq genome • 237 views
ADD COMMENTlink written 6 months ago by colin.kern200

As long as you are on the same genome build changes in the annotation can't be that drastic. Have you compared the annotation you have with the one currently available to find what changed?

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax62k

The reviewers have asked me to include the annotation releases version, so unfortunately this isn't just a matter of convincing myself it doesn't make a difference to the analysis. I agree that the annotation versions shouldn't be significantly different within the same genome build, however the genomes have had new builds recently, so I can't just check if the current version is the same as the one I have and use that version number.

ADD REPLYlink modified 6 months ago • written 6 months ago by colin.kern200

Older genome builds/annotation should always be available. Example archival releases for human genome. Based on the dates on the folders and Readme files you should be able to figure out which annotation you likely used.

If you want to share the genome you are referring to I can take a look.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax62k

Possibly not particularly helpful now, but for future reference: always note down the version number when you obtain data. And maybe send NCBI a grotty email complaining that they didn't put the version number in the file itself.

ADD REPLYlink written 6 months ago by Emily_Ensembl17k

This could give you some clues:

ADD REPLYlink written 6 months ago by Denise - Open Targets4.7k
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