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Old 12-07-2014, 07:33 AM   #1
Ganesh Ujwal
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Default From a list of protein accessions, how can I retrieve DNA sequences from GenBank?

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?
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