Welcome to PerlMonks, sbusi. Note that only some of us are bioinformaticians (I am not), so if you want a broader audience for your question, it would be helpful if you could explain the terminology you're using, and/or describe your question in programming terms. See also How do I post a question effectively? and Short, Self-Contained, Correct Example: showing some short, representative sample input, the expected output corresponding to that input, the code you're currently using, and the current output including any error messages, each within <code> tags, will let more people take a crack at answering your question. Update: And for questions regarding matching, providing several examples instead of a single one is very helpful.