my Profile reply

Michael Gribskov gribskov at SDSC.EDU
Tue May 12 20:32:30 EST 1992


My apologies to those involved in the recent discussion of the use of
the PROFILE* programs.  The recent flurry of interest, unfortunately, 
coincided with my recent move to San Diego, and I have been a little too 
harried to reply properly.  I have a few comments:

	1) The programs are still under active development, and I expect
	to have a new and much improved version available this fall.  
	Now is a very good time to voice your suggestion and complaints.

	2) I currently have about forty of what I call validated 
	profiles (i.e. with known statistical properties).  These will
	be available as soon as I get a chance to properly document 
	them.  Unfortunately my move has disrupted this rather badly.

	3)As I have emphasized to those who have contacted me directly, 
	I have an ongoing interest in assembling a comprehensive library of 
	"validated" profiles. This message has probably not filtered 
	through to the people who use the package soley in its GCG 
	implementation.  PLEASE, if you have developed profiles that you 
	consider to be powerful, send them to me so I can pass them on 
	to others with updates of the programs.  It is also a good idea
	to archive the profiles at a common site (e.g. iubio, uh, embl, 
	etc).

	4) The biggest problem with assembling the profiles is 
	adequately documenting them, At least this has been the rub for 
	me.  I would like to be able to provide for each profile:
		a) the alignment used to make it
		b) list of sequences xrefed to dbs
		c) prose description of function with correct annotation
		   in terms of the multiple alignment coordinates
		d) known statistics from database searches
		e) known false positives/negatives
		f) one or more references (to a review if possible) to 
		   provide a hook into the literature.
	However, do not neglect to send your profile just because you
	don't have the time do all of the above.

	5) There are a couple of improvements to the package since 
	the most recent versions GCG distributes.  The most useful is a 
	version of profilegap that produces a multiple alignment.  If this 
	would be useful to you, please contact me.  It is still a 
	prototype, but seems robust (if clumsy).
	

There is probably more to say on this thread that I have missed in my 
move, but this will do for now.

Michael Gribskov
San Diego Supercomputer Center
P.O. Box 85608
San Diego, CA 92186-9784

(619) 534-8312
gribskov at sdsc.edu





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