Gribskov's profile method: ?'s (also posted w/ INFO-GCG)

dmerberg at GENETICS.COM dmerberg at GENETICS.COM
Thu Apr 16 10:33:26 EST 1992

Hello out there,

Steve Thompson writes:

>for Washington State University.  I am very impressed with its power and
>elegance and have assembled and analyzed many profiles for the various
>researchers that I work with.  However, I perceive a sorely lacking aspect of
>the method in the absence of an algorithm for performing local dynamic
>programming methods between two different profiles.

I have also found profile analysis very powerful in revealing novel
relationships between proteins.  And I have also thought it would be
useful to compare profiles in a quantitative way.  There was a program,
PRALI, by Martin Vingron (CABIOS 1989, 5:115-121) which aligned groups
of aligned sequences quite nicely.  However, it is not in GCG style and
might require too much massaging of sequences between formats for many
people.  Also I'm not sure whether Martin is still distributing it.  A
GCG style program that aligned profiles (or perhaps more conveniently,
aligned MSF files) would be a valuable contribution.  I think I could
write such a beast although there are probably others out there who
could devote more time to it and produce one faster.  If I don't hear
that someone is actively working on one I'll have a try at it.

> is anyone
>or is any archive interested in these profiles as I develop them?  It seems a
>shame to only have them available to the WSU academic community.  Naturally, if
>any of them were to be utilized in anybody's research I would expect
>acknowledgements.  I presently have more than a dozen "high-quality" profiles
>prepared apart from the library already utilized by ProfileScan and am creating
>new ones all of the time.

The more good profiles available the more powerful the technology is. 
I would certainly be interested in having additional profiles in the
library.  Perhaps an archive curator would like to start a collection
from various sources.

Dave Merberg
Genetics Institute
dmerberg at genetics.com

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