[Biopython] CDS location from xml in Biopython

Ara Kooser akooser at unm.edu
Mon Oct 11 20:09:16 UTC 2010


Hello all,

   Thank you again for your help. I have my program up and running.  
One thing that is throwing me is I am trying to extract the location  
of the gene from the BLAST .xml file. I've dug through the .xml and  
can't seem to find the information. Do I need to have the CDS files in  
order to parse the location start and stop values.

So for instance, the record for
modular polyketide synthase [Streptomyces sp. AA4]

before the sequence data is
      CDS             1..5256
                      /locus_tag="StAA4_010100030484"
                      / 
coded_by="complement(NZ_ACEV01000078.1:25146..40916)"
                      /note="COG3321 Polyketide synthase modules and  
related
                      proteins"
                      /transl_table=11
                      /db_xref="CDD:33130"

The start/stop values (25146:40916) aren't in the .xml is that  
correct? So I would need to add a separate code in Biopython to handle  
the CDS files?
Thanks!
Ara



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