Figure 1

Major Focuses in Motif-finding research. The problems of discovering a significant subsequence motif from a set of sequences (A), discovering a candidate list of redundant subsequence motifs from a set of sequences (B), and discovering a non-redundant, condensed motif from a set of redundant subsequence motifs (C) are interrelated. Integrated motif-discovery frameworks seek to perform both (B) and (C), often by combining several tools designed to retrieve a single motif (A). In this description, discovering “one motif” or a “set of motifs” refer to descriptions of a single functionally meaningful phenomenon - in principle, multiple independent functionally meaningful motifs may exist in a sequence data set, however we avoid representing this case in the above figure to avoid confusion.