I am having difficulty with using qblast to search for sequence similarity just in the RefSeq database and hopefully someone can point me in the right direction. My qblast query is formatted like so:
query_handle = NCBIWWW.qblast('blastn', 'refseq_genomic', fasta_string)
This query works perfectly when querying the 'nt' or 'nr' databases, returning an XML object that can be parsed for hits. However, when I try to use the 'refseq_genomic' database field, my XML return object is empty (hitless). I have tried the search manually with the BLAST web interface and gotten the expected results (proper hits). Does anyone what might be causing this problem?