The first step was to research other phenotypical papers produced by other labs to search for viable candidates.
Primarily this meant looking for papers with other test animals, chickens and mice mostly. I would read through the papers repeatedly and write about the prospects for our labs own research in their papers. I would then submit the paper to our team lead or the professor directly to see if there was anything interesting that I or another research assistant found.
The second step to look at the what the linked effect of the gene was on other animals, and see if there were analogous mutations or structures in pigeons.
This would be a comprehensive test first looking at if it was possible for the gene to be linked at all, to looking at the effect the mutation had on the previous animals, to BLASTing the gene in the paper and the pigeon and looking to see if there were similar gene structures. The comparisons would take a while, and we would look into the protein alignment and the FASTA data and see if the pigeon genomes we had contained enough similarity to the genes in the other species to reasonably compare the two.
I would look at the depth file and the SNP file we created to see if any of the bird species had the gene, and then look at the various genes that did exist and compare their phenotypical variation with the variation found in the depth file and SNP data.