Asap is an open source framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.
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Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A:
Asap: a framework for over-representation statistics for transcription factor binding sites.
PLoS ONE 2008, 3(2):e1623