bbq (Barbeques) is a command-line tool for discovering clusters of transcription factor binding sites that occur simultaneously in several genome sequences. Finding such clusters – which are sometimes also referred to as cis-regulatory modules – is done in a multiple-alignment-like fashion by solving a certain combinatorial and geometric optimization problem, the so-called best barbeque problem (explaining the name bbq). As opposed to classical, typically dynamic programming based, alignment procedures, the order of the binding sites’ occurences can be arbitrarily shuffled, so that bbq is the result of developing completely new algorithms.
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