From a list of protein accessions, how can I retrieve DNA sequences from GenBank?

[Ganesh Ujwal]

I have 1000's of protein sequences in FASTA/their accession numbers. I want to go back into the whole genome shotgun database and retrieve all DNA sequences that encode for a protein greater than or equal to 99% identity to my original sequences.

I've tried running a tBlastn with <10 results for each sequence, 1 per query and e-value below 1e-100 or with an e-value of zero and I'm not getting any results.

Is this even possible, or is the WGS too much of a mess?