Biopython blastn speed versus web query
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9 weeks ago
nu2000 • 0

I wonder if anyone can help me. I'm experiencing big performance problems when running a BLAST query in biopython. I have a sequence of about 1000 nt (see below) which I am trying to run blastn.

When I run this in biopython, occasionally I get something back in about 60 seconds [usually the first time I run it], but more often than not, it just seems to run forever

result_handle = NCBIWWW.qblast("blastn","nt",frag_2)
blast_record = NCBIXML.read(result_handle)

But when I paste the same sequence into the Blastn web tool directly, I get results back in about 15 seconds each time. Am I doing something wrong?

TGACCGGCGCGTTGTTGACGGTGGTGCCGTTGGTCGAATTCAGGTCCGACAGCAGCGCGGCATGCCCGTCGAAGCGCACCTCGAGGTGGCGGCGCGAGACGCCGGTATCGGGCAGACGGAACTGCGCGTCCTGACCGCGGCCGATCACATTGGTGCCCTCACGCAACTGGTACGTGCGTCCGCTGCCGTCGTCCAGCTGCAGGGTGACGGTGGTGCGACCGGCACCGGCGCCGCCTCCAGTGGGAGCGCCGTAGTCGGGGCTGCTCTGGTAGCCGCCGTGCTCGTAGTCGCCGTACTCGGGCTCGCCGTAACCGCCCTGAGGTGATCCGTAGCCGCCCTGCTGCGGCGGGGCGCCGTAGCCACCCTGCTGCGGGTAGGCCGGGGGACGACCGTAGTCCTGGCCCGGAGGCGGACCCTGCGGTGCGCCATAGCCACCGCCCTGTTCGTACTCGCCGTAGTTGGGACGAGGAGGCTCGCCGTACCCACCCTGTTGCGGCGGGGCGCCGTAGCCGCCCTGCTGCGGAGGTGCCGGGGGACGGCCGTATTCCTGACCGCCGCCATAGCCGCCCTGCTCATAGCCACCGCGGCCGCCTTGGTCGTAGCCACCCTGCTGTGGCGGGCGCTGTTGGTAGCCGCCCTGCTCATAGCCGGCCGGTGGGCGACCGTAATCCTGCCCGTACTGCTGGCCCTGCCCATATCCGCCCTGGCGCGGGGGGTATCCCTGGTCACCCTGCGGAGGCTGCTGACCACGTGGATCCTGTTCGGGACGTCCGTAGCGGTCGTCCTCTCGGCCGTACTCTTCGCCGGGGCGTCCCTGCTGGGGACCTGGGTTGTCAGTCATGGATGCTCCTGGTTGTGGATCCGGGGTCGAAGGGGCAGTCGTCACGGCGCCGTGCGTACGGTCCCGCTTGGTGTCGGGATTGACCACACCGCGCGTGCGAAACTGGCCGGTGTGCAAGTTCGGTGATTGTTCGAATCGGACAACAACTTCACCATACGT
blast biopython • 211 views
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you should also provide the cmdline (parameter settings you are using here).

Also keep in mind that the NCBI webblast likely uses different settings (and resources) than local blasts.

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Hi, I'm not using cmdline. This is the full program essentially.

from Bio.Blast import NCBIWWW, NCBIXML result_handle = NCBIWWW.qblast("blastn","nt",frag_2) blast_record = NCBIXML.read(result_handle)

where frag_2 is the string of characters. My understanding was that this effectively calls the website (I don't have a local blast installed). As I say, it sometimes works, but more often than not, just looks like it's running for a long time (I suspect there may be an issue with the sleep settings)

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OK, so you might be using default parameters.

If you are using the webblast extensively, keep in mind you are only allowed to run a number of jobs in parallel and also a max number of jobs a day (I think 100 ). If you violate those limits they will start putting you down in queue or ultimately block you.

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