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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Genomes for performance tests