[Owl-devel] Blast parsing bug

Jose M. Duarte jose.m.duarte at gmail.com
Thu Apr 22 08:30:01 EDT 2010

Hi all

Just to let you know, now that you are doing CASP this might be important.

I've just fixed a bug in the blast XML parser to properly get the subject id
from the Hit_id XML field instead of from the Hit_def field. I've just
realised that before we were running formatdb without the "-o T" option
which tells blast to generate indices based on the fasta tags. Then the
Hit_def had the pdb id that we were interested in so everything was working
fine, but that's not really the right way to do it (I've realised this now
when trying to blast against uniprot).

So conclusion is: use the "-o T" option from now own when formatting blast
databases with formatdb. The casp tools should then work as usual.

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