SWAN (Stubb With Another Null) is a software to meant for genome-wide prediction of regulatory targets of a motif using a Hidden Markov Model. It differs from Stubb in that instead of asking Does the sequence have more sites than expected from a random (background) model of sequences?, it asks the question Does the sequence have more sites than the average genome-wide frequency of sites?
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PLoS Comput Biol. 2010 Jan 29;6(1):e1000652. doi: 10.1371/journal.pcbi.1000652.
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.
Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S.