[BioPython] pblast in NCBI's website differs from biopython's pblast

[Raul Guerra]

Hi everyone,

I was wondering if someone has had the same problem. I am running the
following code in BioPython.

        result_handle = NCBIWWW.qblast("blastp", "nr", fastaStr,
entrez_query='"Chlamydomonas" [ORGN]',ncbi_gi= True,matrix_name='BLOSUM62',
hitlist_size=50)

where fastaStr is the fasta string for NP_012855. (When I mention
Biopython's pBlast I refer to the code above)

The results that I got back are different from the results I get from the
pblast option  at http://www.ncbi.nlm.nih.gov/blast/Blast.cgi , if you
follow the link click on pblast and do a blast just specifiying the organism
and the sequence accession number.

The results that I got from NCBI's website are 2 sequences, which were what
I was looking for. On the other hand, Biopython gives back as many hits as I
specify in the limit. Also in Biopython's pBlast, I only get one of the hits
that I get in NCBI's pBlast. I know that the qBlast option in NCNBIWWW has
many parameters.

def qblast(program, database, sequence,
           auto_format=None,composition_based_statistics=None,
           db_genetic_code=None,endpoints=None,entrez_query='(none)',
           expect=10.0,filter=None,gapcosts=None,genetic_code=None,
           hitlist_size=50,i_thresh=None,layout=None,lcase_mask=None,
           matrix_name=None,nucl_penalty=None,nucl_reward=None,
           other_advanced=None,perc_ident=None,phi_pattern=None,
           query_file=None,query_believe_defline=None,query_from=None,
           query_to=None,searchsp_eff=None,service=None,threshold=None,
           ungapped_alignment=None,word_size=None,
           alignments=500,alignment_view=None,descriptions=500,
           entrez_links_new_window=None,expect_low=None,expect_high=None,
           format_entrez_query=None,format_object=None,format_type='XML',
           ncbi_gi=None,results_file=None,show_overview=None
           ):

I also know that the pBlast in NCBI's website utilizes a Gap Cost of
"Existence: 11 Extension:1". I am not sure how to translate that into the
qblast function in Biopython. I am not sure if this is the problem, but it
could be that Biopython's pblast and NCBI's pblast have different
parameters.

Thank you for your time,

David