#15 install the new version of pfam_scan.pl
Sam has written a new version of pfam_scan.pl which
runs faster. On their test set it gives the same answers
as the old version, but he does expect it very
occasionally to miss some hits to specific families.
These families are the very short things like the XYPPX
repeat.
The new version con be downloaded from
http://www.sanger.ac.uk/Users/sgj/code/ - he is making
this available to people outside as well. When he
updates the script he will notify us so we can get the
latest version.
The script needs a copy of the Pfam flatfiles - having a
local copy would be best. Sam and Hans could arrange
for us to have a mirrored version on babel.
Once installed people can test it and give their feed-
back to Sam. The options have changed significantly -
you need to point the script at the Pfam data with the -
d option, and then you want to use --fast to get the
speed-up. It should be ~10x as fast as the old version.
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The script is installed as /pfam/db/Pfam/bin/pfam_scan.pl
I haven't tried it but you'll need to give a database on the
command
line:
/pfam/db/Pfam/bin/pfam_scan.pl -d /data/blastdb/Pfam/