Synteny test and tools to use for mammalian organisms?

Question

I am trying to do a synteny test for MHC genes in human and another mammalian organism

For this reason, I need to download all paralogs of rabbits from humans and then construct position the coordinates of paralog to test the synteny. However, I am unsure how to download the paralogs from Ensembl and how to perform this test?

My main aim is to research synteny between MHC genes of humans, rabbits and mice.

Any suggestions on how to do this or alternative bioinformatic methods on how to perform a synteny test would be highly appreciated!

Answer 1

This is not an easy ask. Firstly, very few species (I think only human and mouse) have alternative haplotypes annotated for MHC. Most species only have the primary assembly, only one possible haplotype of this locus. This means that the haplotype in the primary assembly is not necessarily the same haplotype as you'll find in another species. Since the MHC haplotypes can contain completely different genes, you will necessarily be able to find orthologues and synteny.

Secondly, we in Ensembl do not calculate homologues of the genes on the alternative loci, so we only have homologues of the genes that just happen to be on the primary assembly.

There is already pre-calculated synteny in Ensembl. Here's the human MHC locus compared to Rabbit. This includes all the homologous genes across this locus. However, this is just one arbitrary MHC vs another arbitrary MHC.