Hello Bradley,

Although you can include those ambiguous codes in the input for BLAST, they will be treated as mismatches in the alignment. So, they are not totally ignored, instead you can think of it as if they were gaps.

You can read more about this here: 

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp

I hope that helps.

Best regards

problem can be resolve by biopython alphabets 

http://biopython.org/DIST/docs/tutorial/Tutorial.html

and if u look for the Substitution Matrix for  IUPAC Nucleotide Ambiguity Codes - NUC.4.4

ftp://ftp.ncbi.nih.gov/blast/matrices/NUC.4.4

Thank you for the responses. It turns out that BLAST will include (and 'interpret') IUPAC ambiguity codes for a nucleotide BLAST, but will discount them for a protein BLAST (where codons are needed rather than nuceotide bases) - makes sense!