Closest Strings, Primer Design, and Motif Search

Spurious Motifs.Our algorithm finds all positions in the strings that meet the specified requirements and will report no positions that do not; this is its advantage in contrast to algorithms in [5] and [3]. However, it clearly cannot exclude to find spurious motifs, e.g., random motifs in artificially generated data that have not been implanted. Note that not all combinations of L and d values are reasonable; if d is chosen too large compared to L, we can expect spurious randommotifs [3], e.g., with 20 random sequences of length 600, one can expect at least one (15, 5)-motif.