[Biojava-l] Ambiguity consensus string search

[Charles Danko]

Hi,

I'm trying to search a Sequence or SymbolList object for a consensus
sequence that contains IUPac ambiguity codes.

Without ambiguity codes, I could write a function that breaks the sequence
into "windows" the size of the consensus, and checks each window for a
match.  Am I missing a simple function that does this for me?

Next, adding ambiguity codes ... do I have to define my own alphabet for the
DNA IUPac codes, or are these already included in the distribution
somewhere?

I have found the weight matrix class, and realize that I could create one of
these objects and calculate a threshold that will work in the same manner as
a consensus, but this seems like a bit of a hack for some functionality I am
most likely overlooking.

Thanks very much!

Charles