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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
