Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference

Journal of Molecular Evolution
Christoforos Nikolaou, Yannis Almirantis

Abstract

The distribution of n-tuplet frequencies is shown to strongly correlate with functionality when examining a genomic sequence in a reading-frame specific manner. The approach described herein applies a coarse-graining procedure, which is able to reveal aspects of triplet usage that are related to protein coding, while at the same time remaining species independent, based on a simple summation of suitable triplet occurrences measures. These quantities are ratios of simple frequencies to suitable mononucleotide-frequency products promoting the incidence of the RNY motif, preferred in the most widely used codons. A significant distinction of coding and noncoding sequences is achieved.

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Citations

Aug 2, 2005·Journal of Molecular Evolution·Christoforos Nikolaou, Yannis Almirantis
Feb 9, 2010·Bioinformatics and Biology Insights·Nicolas CarelsDiego Frías
Feb 9, 2010·Bioinformatics and Biology Insights·Nicolas Carels, Diego Frías

Related Concepts

Sense Codon
Oligonucleotides
Unassigned Reading Frames
Computational Molecular Biology
Online Mendelian Inheritance In Man

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