[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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