Annotate GWAS result gene function from GFF file

Question

[alnus]

Hello everyone. I am trying to annotate the function of gene of Tectona grandis (teak) from GWAS result using the GFF file provided by the genome reference creator. I tried some tutorial and web searching, but I couldn't find a tutorial that is suitable for my analysis. I think since I am nnew to this field, I need someone to thow the light. I am in a point that I can extract the GWAS result and find the gene parent and its ID. However, how to use after I find the ID is really challenging.

Here is my ID example and trying to find their gene function, is that possible?

Answer 1

[lieven.sterck]

If the info you need is available in the GFF file then yes it is possible, however according to GFF specs it is not a necessity to put this kind of info (functional gene info) into the GFF file.

if it is there you can simply use grep with the parent geneID on the GFF file (eg. : grep Tecgr32502629_TECGRA <GFF file>) . this will return all the lines with that geneID on it in the GFF file, if too many are returned you can even expand the grep function, for instance add | grep 'gene' or such to more focus on the lines with the gene info on it.

If this would not work, due to missing gene functional info in the GFF file, you could have a look at the protein fasta file if that is provided, because sometimes there is some functional info on those fasta headers as well.

[alnus]

Thank you very much I think it cannot be possible since the owner of gff file do not attach any function in it. However, I would like to try search their gene function the closest possible match using public data base.

[lieven.sterck]

that certainly is an option indeed. Just running a blast against nr-prot DB of NCBI and investigating the best hit(s) is a way to go (bit crude but workable) . A bit more advanced would be for instance to run an InterPro analysis.