Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning | Zendy

Raffaele Giancarlo | Zendy; Simona E. Rombo | Zendy; Filippo Utro | Zendy

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Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning

Author(s) -

Raffaele Giancarlo,

Simona E. Rombo,

Filippo Utro

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv295

Subject(s) - nucleosome , epigenomics , chromatin , computational biology , composition (language) , biology , r package , computer science , k mer , variety (cybernetics) , dna sequencing , evolutionary biology , genetics , dna , artificial intelligence , gene , dna methylation , linguistics , gene expression , philosophy , computational science

Information-theoretic and compositional analysis of biological sequences, in terms of k-mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k-mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open.

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