Epigenomick-mer dictionaries: shedding light on how sequence composition influencesin vivonucleosome positioning

• DOI: 10.1093/bioinformatics/btv295
• Publication Date: 2015-05-26T00:31:00Z
• Authors: Raffaele Giancarlo; Simona E. Rombo; Filippo Utro
• Keywords: Epigenomics; R package; k-mer

Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms k-mer dictionaries, has a well established role genomic proteomic studies. Much less so epigenomics, although the k-mers chromatin organization nucleosome positioning is particularly relevant. Fundamental questions concerning informational content structure favouring disfavoring sequences with respect to their basic building blocks still remain open. Results: We present first on composition enriched depleted regions (NER NDR for short) that is: (i) exhaustive within bounds dictated by information-theoretic sample sets we use (ii) informative comparative epigenomics. analize four different organisms propose paradigmatic formalization providing two complementary views involved NER NDR. The extends known studies this area, its nature being major merit. second, very novel, brings light rich variety influencing positioning, which an initial classification clusters also provided. Although such offers many insights, following deserves be singled-out: short poly(dA:dT) tracts are reported literature as fundamental depletion, however global quantitative look reveals much prominent than one would expect based previous Availability implementation: Dictionaries, Supplementary Material available online at http://math.unipa.it/rombo/epigenomics/. Contact: [e-mail] information: data Bioinformatics online.