[bip] online sites for doing binding site search

[Titus Brown]

On Fri, Nov 30, 2007 at 05:13:06PM -0800, Erich Schwarz wrote:
-> On Fri, 30 Nov 2007, Titus Brown wrote:
-> 
-> > Maybe I'm going one level more cynical than you, but I also think
-> > the dearth of effective tools (and the ubiquity of mediocre ones)
-> > points to the difficulty of the problem.  So the opportunity has
-> > to be weighed against the likelihood that this is just a real hard
-> > problem...
-> 
->     What I liked about the Wasserman and Sandelin review (aside from
-> the fact that it is the *only* review I have yet found that actually
-> bothers to clearly and correctly explain the differences between
-> PFMs, PWMs, PSSMs, PSFMs, etc. etc.), is that they actually do cover
-> cluster-searching and explain why it's nontrivial.

I'm immensely frustrated with this (very good) review, because it's so
bloody computationally oriented.  Ahh well, who cares what biologists
actually need, or how cis-regulation actually works?? ;)  It does help
convince me that there's useful work to be done in this field, and not
only on the "pretty shiny" GUI front.

Anyway, having read the paper thoroughly,

	PFM, position frequency matrix; what I've been calling PWM.

	PWMs == PSSMs, log of PFM; reverse of "energy operators".

	PSFM is not mentioned at all, presumably == PFM.

Humm, maybe I should revisit the motility tutorial and documentation
with these definitions in mind...

cheers,
--titus