[BioPython] NCBIXML Blast parser Error for TBLASTN

Alaguraj Veluchamy alaguraj.v at gmail.com
Tue Apr 8 19:29:52 UTC 2008


Dear people,I am stuck in parsing Blast XML output.
I am trying to extract the co-ordinate and hence the sequence of the hits
for my query in standalone blast.
XML output is coming for query proteins against a genbank genome file.
(using TBLASTN)
The problem for me is- I am unable to get the co-ordinate(hit-from -->
hit-to).
I used hsp.sbjct_start and hsp.sbct_end, but it gives two numbers which is
different from the original.
when i tried extracting those regions from the genbank file and do an
alignment, it nowhere matches.
so what is this hsp.sbjct_start - integers?? how to get the hit region (or
alignment) cordinates?
I read record.py--the library file, but they given it is 3x times larger
(but still it is incorrect)
Regards
-Alaguraj.V



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