Setting the window size is always a bugaboo. There is
a little bit of literature on it. Try in SeqAnalRef, a
bibliography on sequence analysis maintained by Amos Bairoch,
available via http://expasy.hcuge.ch/
Some additional options include:
1) Changing the windowing function. Most programs
use a "square-wave" -- either something is in
the window or it isn't. Various other functions
might be used which weight data at the outside
of the window less than data in the center.
2) Computationally exorbitant, but possibly elegant,
is to look at _every_ window size. I.e., draw
a 3D plot of value vs. position vs. window size.
Good luck!
Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu
