Does Biopython.Blast allow you to read nucleotide sequences with ambiguous bases?

Question

[Airhead]

Hello!

I am getting the error message "Message ID#24 Error: Failed to read the Blast query: Protein FASTA provided for nucleotide sequence" when trying to run qblast, and I have a feeling it is due to the N's representing an ambiguous base in the sequence. Is there a way to resolve this issue?

[Mensur Dlakic]

Is there a way to resolve this issue?

There should be an easy way. Without changing your code, give it a sequence that doesn't have any Ns in it. If the code runs, Ns are the problem. If it still doesn't run, it could be the code or it could be Ns. The point is to get the code running without Ns and then test again your original sequence.

[Joe]

Can you share the exact command you're using? Are you passing a sequence string, or another BioPython object like a SeqRecord?