[Biopython] Qblast : no hits

[Karthik Raja]

Hello freinds,



I have a  problem with qblast. I have sequences from the mass

spectromerty equipment that needs to be BLASTed to find the protein it
belongs

to. When I blast these sequences in the NCBI website it takes some time

(longer than usual ) but does gives me hits. When i blast them using the

following code in biopython they dont give me any hits.



CODE:

****************************************************************************

>>> from Bio.Blast import NCBIWWW

>>> result_handle = NCBIWWW.qblast("blastp", "nr", "AFAQVRCSGLARGGGYVLR")

>>> blast_results = result_handle.read()

>>> save_file = open( "testseq.xml", "w")

>>> save_file.write(blast_results)

>>> save_file.close()

****************************************************************************



OUTPUT:

****************************************************************************

<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI

BlastOutput/EN" "NCBI_BlastOutput.dtd">

<BlastOutput>

  <BlastOutput_program>blastp</BlastOutput_program>

  <BlastOutput_version>BLASTP 2.2.23+</BlastOutput_version>

  <BlastOutput_reference>Alejandro A. Sch&auml;ffer, L. Aravind, Thomas L.

Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and


Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein

database searches with composition-based statistics and other

refinements", Nucleic Acids Res. 29:2994-3005.</BlastOutput_reference>

  <BlastOutput_db>nr</BlastOutput_db>

  <BlastOutput_query-ID>12361</BlastOutput_query-ID>

  <BlastOutput_query-def>unnamed protein product</BlastOutput_query-def>

  <BlastOutput_query-len>19</BlastOutput_query-len>

  <BlastOutput_param>

    <Parameters>

      <Parameters_matrix>BLOSUM62</Parameters_matrix>

      <Parameters_expect>10</Parameters_expect>

      <Parameters_gap-open>11</Parameters_gap-open>

      <Parameters_gap-extend>1</Parameters_gap-extend>

      <Parameters_filter>F</Parameters_filter>

    </Parameters>

  </BlastOutput_param>

<BlastOutput_iterations>

<Iteration>

  <Iteration_iter-num>1</Iteration_iter-num>

  <Iteration_query-ID>12361</Iteration_query-ID>

  <Iteration_query-def>unnamed protein product</Iteration_query-def>

  <Iteration_query-len>19</Iteration_query-len>

<Iteration_hits>

</Iteration_hits>

  <Iteration_stat>

    <Statistics>

      <Statistics_db-num>10888645</Statistics_db-num>

      <Statistics_db-len>-585703444</Statistics_db-len>

      <Statistics_hsp-len>0</Statistics_hsp-len>

      <Statistics_eff-space>0</Statistics_eff-space>

      <Statistics_kappa>0.041</Statistics_kappa>

      <Statistics_lambda>0.267</Statistics_lambda>

      <Statistics_entropy>0.14</Statistics_entropy>

    </Statistics>

  </Iteration_stat>

</Iteration>

</BlastOutput_iterations>

</BlastOutput>

*****************************************************************************





Is this because a normal blast code doesn wait long till the results are

given? I mean the RTOE error. if yes, how to control the "time of
execution"?

Or else what is the problem with my code?

If you guys know anything on this issue, please give me your ideas.

Thanking you in advance.

Sincerely,

Karthik