My analysis is about whole genome sequencing (Illumina Miseq) of 8 isolates of a parasitic species belongs to two different sub-strains.
I'm concerned with highly variable gene copy numbers among the two sub-strains. I want to do a gene ontology analysis of the set of genes with highly variable copy numbers among the two. This is where I faced the problem. I tried using PANTHER, AMIGO2, GO Consortium but unable to come up with a result. My species is Leishmania donovani and the said databases use Leishmania major genome.
If anyone familiar with GO analysis please advice how to perform it correctly and good tools to use with my species, since I'm new to this type of analysis.
Thanks in advance Rangi