Hi, I have discovered a little inconsistency in biomart.
Usually, the orthologs between two species are stored in a mart called compara_speciesx_speciesy_orthologs, where speciesx and speciesy are sorted alphabetically. There is at least one exception: fly-zebrafish orthologs are stored in compara_drer_dmel instead of compara_dmel_drer. ( You aren't creating all these databases manually, are you?? :-) ) I'm using scripts that access biomart, so I've stumbled over this and added various "if...then"s as a walkaround in my scripts. cheers, Max
