[Biopython-dev] Possible problem with NCBIStandalone.blastall

[Sebastian Bassi]

When I run a command line blast with these parameters:

/root/blast-2.2.18/bin/blastall -p blastn -d /var/www/blast/db/UniVec
-q -5 -G 3 -E 3 -F "m D" -e 700 -Y 1.75e12 -i tmpsq

I find a match (with evalue of 18).
But when I do it from biopyhon I can't find any match:

rh, eh = NCBIStandalone.blastall(blast_exe, "blastn", db,
                                     fin, nuc_mismatch='-5',
                                     gap_open = '3',
                                     gap_extend = '3',
                                     search_length = '1.75e12',
                                     expectation='20')

Here is the input sequence:

>C07SpCP042I015.P5A02.R. [Clone-lib=pCLD 04541]
NNNCCCCCCCTCGAGGTCGACNNNNNNNNTAAGCTTGAAATTCTATGATATGCAGTTAGT
TGCTNCTNGTTTAGCATTGGTTGGTTAACTTAAAACCTTTTCCTGCAATAATTATATGGA
TAATATTACTTTACTTNNNNNNNTATTGCCTTCACTAATTTTTAGGATCTATTTTCTGTT
AAATGTTATCTCTTGTTCTTGAGAAGTGCTTTGGAGATCATTTTTCCATCGTATTAACAA
AAAGTGAAATAACTACTTGTGCAATCAGGCTTTTCCTACACCAGGGGATAAGGCAAATAA
ACTATTCACCTCCTTTAATTAGCTCCCCCCCCCCCCCCTCCCCTTCTTTTCTCTTCATTC
CTGANNNANTTAGCTAGTACGCACCATTCAATCAATTATTTCTGTTCCATTTTGTGCTAA
ATATGTTTTCAAATGTTTAATATAGTTCTGAAGACAGCAGTTTAATGTTTTGTCTGGCTA
ACTGCTATTCTAAGCTCATTGTTTCAGCTTGCAGTTTTGCAGCAAAACCTGTCTGCTGTC
CATGAAATCTGGAAGGAATGTAGTAAATTTTACAGTCTCAGCCTTCTATCTCTGAGGAAG
TTTATATGGTCCTTCACGGAGCTGAGAGATCTGAATTCAGCCCACACAGCCTTACAGCAC
ATGGTGAGATTGGCTTTTACGGAAAACTCTTACATTAGTAGAACTGCTGAGGGGAGGTTT
TGTGATTTAAGATTGGATATTCCAGCACCTTCCTCTGGCAATTGGAGTTTCATCGATGTA
TCTGTCGACACCGCGGGTAGCAGCAATTTTGATATGGAAAGACAAAGTCTTGGCAGAAAA
ACA

and here is the database:
ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec

(I got the parameter from
http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen_docs.html#Parameters)

Best,
SB.


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