Hello Charles, You may find the org.biojava.utils.regex package useful in this regard:
> http://www.biojava.org/docs/api15b/index.html michael Charles Danko wrote: > 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
