Does anybody know how to get untranslated DNA sequences from tblastn in local mode?
This is trivial to do online at NCBI, you just select several target sequences and download them, and what you get are the nucleotide sequences.
However, when running tblastn in standalone mode the output is always translated, and I can't find a way of getting the nucleotide sequences directly.
Somebody asked a similar question here, but I don't think it ever got answered (one of the answers claimed it was a problem with the XML output, but indeed I find it with every output I've tried: they either have protein sequences, or no sequences at all).
Naturally, I could extract the nucleotide sequences one by one from the identifier, start, end, and frame, but one would think there should be an easier (automatic) way.