Can someone tell me how I can perform a BioJava 1.4pre1 regex search using ambiguous symbols?
I'm using the following ambiguous DNA symbols: (http://rebase.neb.com/rebase/link_withrefm) -R = G or A -Y = C or T -M = A or C -K = G or T -S = G or C -W = A or T -B = not A (C or G or T) -D = not C (A or G or T) -H = not G (A or C or T) -V = not T (A or C or G) -N = A or C or G or T If correct, to perform a BioJava-Regex, I need to make a PatternFactory using the following method: FiniteAlphabet fa = DNATools.getDNA(); org.biojava.utils.regex.PatternFactory.makeFactory(fa) So I need a FiniteAlphabet containing ambiguous symbols right? How can I make such FiniteAlphabet? My goal is to perform a searchpattern like "g[agr]cg[cty]c" on a SymbolList like "ATGCGACGTCTTAANNNNNNATGCAAC"; Thanks. -Jesse _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
