A compression-based approach for coding sequences identification in prokaryotic genomes

Menconi, Giulia and Marangoni, Roberto (2005) A compression-based approach for coding sequences identification in prokaryotic genomes. Technical Report del Dipartimento di Informatica . Università di Pisa, Pisa, IT.

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Abstract

To identify coding regions in genomic sequences represents the first step toward further analysis of the biological function carried on by the different functional elements in a genome. The present paper presents a novel method for the classification of coding and non-coding regions in prokaryotic genomes, based on a suitable defined compression index of a DNA sequence. The proposed approach has been applied on some prokaryotic complete genomes, obtaining optimal scores of correctly recognized coding and non-coding regions. Several false-positive and false-negative cases have been investigated in detail, discovering that this approach can fail in the presence of highly-structured coding regions (e.g., genes coding for modular proteins) or quasi-random non-coding regions (regions hosting non-functional fragments of copies of functional genes; regions hosting promoters or other protein-binding sequences, etc.).

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