KIRMES(Kernel-based Identification of Regulatory Modules in Euchromatic Sequences) is a new algorithm that combines the benefits of existing motif finding with the ones of Support Vector Machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana we were able to show that the newly developed strategy significantly improves the recognition of transcription factor targets.
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KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G.
Bioinformatics. 2009 Aug 15;25(16):2126-33. Epub 2009 Apr 23.