WRT to Pfam - are you using the old 2.1 release or the 3.0 bbeta
release - 3.0 beta release has a different format, and annoyingly we have
soem direct links from Pfam to prosite profiles which are considered
by prosite/srs as the same thing as prosite patterns.
(the problem is that if you put a direct link from prosite to
pfam using that you only end up with 6 entires, whereas
prosite>prositedoc>pfam is much close to 600!)
Just for your info
Ewan Birney
<birney at sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/
