[bip] online sites for doing binding site search

[Erich Schwarz]

On Fri, 30 Nov 2007, Titus Brown wrote:

> I thought PFMs, PWMs, PSSMs, PSFMs, and energy operators were all
> mathematically equivalent to a zeroth order Markov Model.  Hmm.

    I believe they all *are* examples of zeroth order Markov Models.
However, there are differences in the way their matrix values are
computed that aren't trivial.

    Another article that I thought did a good job of explaining the
theoretical justifications for the different scoring schemes used in
PFMs, etc., was:

    Stormo, G.D. (2000). DNA binding sites: representation and
discovery. Bioinformatics 16, 16-23. [PMID: 10812473].

    http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/1/16


--Erich