ALSE (ALl SEquences) compares favorably against common motif-finding programs such as SeedSearch and MEME in all cases and performs very well, especially when each input sequence contains more than one binding site.
Bioinformatics Research Group of Hong Kong University
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Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.
Finding motifs from all sequences with and without binding sites.
Leung HC, Chin FY.