[Biopython-dev] [BioPython] [Biopython] Blast problem

Peter biopython at maubp.freeserve.co.uk
Tue Jan 15 09:09:47 EST 2008


Hi Joost,

> Iam having a problem with the hsp.match function in the Bio-Python Blast
> module. A few weeks ago the hsp.match returned me the following:
>
> ATGGCA++TGG
>
> But now it gives me:
>
> ATGGCA TGG
>
> I can't see the number of gaps anymore, anyone a solution for this?

Are you using the online version of blast with Biopython?  Perhaps the
NCBI changed something.  Are you parsing the XML output or the plain
text?  Can you provide any more information (e.g. which version of
Biopython).

Thanks

Peter


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