[Bioperl-l] New RefSeq WP_XXX series Sequences

[Warren Gallin]

Hi all.

	NCBI has started a new class of protein entries in the bacterial and archaeal organisms.  These protein records have no direct reference to the underlying nucleotide sequence in the GenPept record, and when I ran some tblastn runs some of them do not even yield a hit to a 100% identical sequence.  I just ran an update script that I use for populating a database of voltage-gated potassium channels, and of the >1400 protein records that I retrieved as GenPept format records, 3338 had a link to a nucleotide sequence record.

	Has anyone encountered this problem, and if so have you found a way of finding the nucleotide sequences corresponding to this class of protein records?

Thanks,

Warren Gallin