[Bioperl-l] Method dnaseq in EncodedSeq not working properly?

[Aaron J. Mackey]

You're completely correct, it's entirely documented but entirely 
unimplemented.  Since you're the first to notice, you must also be the 
first to need it ;)  If you continue to need it, I'll see what I can do.

> Actually, what I really need is a way to identify pieces of repeated 
> X's or N's from DNA sequences in order to exclude them from a 
> sequence-wide screening for good hits of a position-weight-matrix.

If I understand you correctly, your weight matrix search results in 
hits that "align" against X/N's, and you want to filter out those hits. 
  I see two choices:

    1) alter your profile to give very bad scores to X/N (if you have 
this capability)
    2) use some Bio::Range objects representing hits and X/N stretches, 
and call
       $hit->overlap($xn) to see if they overlap.

-Aaron