An Alternative Approach to the Genomic Signature Representation

N. De Giacomo and F. de Santis (Italy)


genomic signature, relative abundance, chaos game, polynomial interpolation.


Extensive data analyses concerned with genome sequences support the proposal that each living organism is characterized by a genomic signature consisting of oligonucleotide relative abundance values calculated from genomic sequences. Then, in order to determine oligonucleotide frequencies, the rough counting of subsequences of a long DNA sequence showing specified features is requested. However, such a counting is well suited only for words of length less or equal than four nucleotides. For longer words a more tractable tool derived from the “chaotic dynamical system” theory (the so-called Chaos Game Representation, for short CGR) is used allowing the frequencies of oligonucleotides to be depicted in the form of fractal images. Using CGR, experimental results show evidence of the fact that the core features characterizing the whole genome are preserved in short subsequences of it, validating the idea of a genomic signature. This paper present an alternative approach to the genomic signature representation and analysis. Although ensuring the same information retrieved from the classical methods known in the current literature, it presents the advantage to be conceptually very simple and computationally less expensive and tractable.

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