Dear Monks,

Thanks for all your explanations. I think the answer is as simple as Ikegami and BioLion state it: it is likely that there are two sequences with the same name. I shall check this before I try any more complicated solutions.

@ BioLion: verbose lives in Bio::Root::Root. I am not using it, the default level works for me.
@ Khen1950fx: I did find the PrimarySeq _seq method, but that only lives in the Corba version and I only use the bio-perl-live packages.

You have all been very helpful!
Wil