Entropic Profiler

Entropic profiles of DNA sequences are local information plots of the relative over and under-expression of motifs per position. They are calculated based on Chaos Game Representation (CGR) using a recently proposed fractal kernel and Parzen's window density estimation method. They allow the visualization of motif densities for two different parameters: resolution L and smoothing parameter Φ. This method detects biological significant regions of DNA, here exemplified for the genomes of E.coli and H.influenzae and promoter regions in B.subtilis. An important simplification allows its calculation using segment counts, explored in this application through suffix trees.
Vinga, S. and Almeida, J.S.: Local Renyi entropic profiles of DNA sequences. BMC Bioinformatics 2007, 8:393.
Fernandes F., Vinga S., Freitas A.T., Almeida J.S.: Entropic Profiler - detection of conservation in genomes using information theory. BMC Research Notes 2009, 2:72.

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