I have been stuck here for quite a long time. I would be really grateful if someone can help me out.
I have a list of thousands of SNP sites in human (BED format), which are all located in CDS region. I want to know what is the corresponding sites in other species, the whole codons containing these sites in all 46 vertebrate species.
I know ensembl already provided the alignment of all 46 genomes, but how could I know the exact codons?
Can anyone tell me how to do this by using ensembl or if this can be done by writing some programs, can anyone help me with the algorithm?
Thanks a million!