How to identify corresponding chromosomes and coordinates of a species for query genes from a another species

Question

[majeedaasim]

I have a gene list of species A and reference genome and gff3 of species B. I want to know the homologous genes of species A genes in species B genome. I am specifically interested in knowing the chromosomes and coordinates of species B homologs. If I use BLAST, then in the output format there is no information on chromosome and coordinates of the subject. How could this be achieved?

Answer 1

[kashiff007]

There are plenty of tools to this, depending on what you want to achieve. In your case what I understand that you have GFF files from both the species A and B, which means you have the sequences of gene sets from both the species. So I suggest you to use MCScanX which is highly cited paper to detect the orthologs.