Question: (Closed) Problem using Biopython qblast (NCBIWWW) with refseq_genomic database
gravatar for Spencer D.
2.4 years ago by
Spencer D.0
United States
Spencer D.0 wrote:

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?


blast python genome • 1.2k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Spencer D.0

Just a quick bump. If this is too general of a question let me know and I can dive a little more deeply in a few directions,  but it would be great to know where someone with more experience might think the issue lies.

ADD REPLYlink written 2.4 years ago by Spencer D.0

UPDATE for anyone who has struggled / may struggle with this issue in the future

A field I hadn't looked at in my XML output, <Iteration_message>, held an error:

<Iteration_message>[blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).</Iteration_message>

So apparently my error with BLASTing was not due to poorly formatted requesting (to my knowledge), but with my account/ip/email running out of allotted CPU time.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Spencer D.0

Did you use a delay function to get around this problem?

ADD REPLYlink written 23 months ago by wardaustin400
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