What is it about?
In this report, we revisited simple features that allow the classification of coding sequences (CDS) from non-coding DNA. The spectrum of codon usage of the sequence sample considered was large and suggested that these features are universal. The features that were investigated combine (i) the stop codon distribution, (ii) the product of purine probabilities in the three positions of nucleotide triplets, (iii) the product of Cytosine, Guanine, Adenine probabilities in 1st, 2nd, 3rd position of triplets, respectively, (iv) the product of G and C probabilities in 1st and 2nd position of triplets.
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Why is it important?
These features are a natural consequence of the physico-chemical properties of proteins and their combination is successful in classifying CDS and non-coding DNA (introns) with a success rate >95% above 350 bp. The coding strand and coding frame are implicitly deduced when the sequences are classified as coding. The method does not need any training step.
Perspectives
It is expected that the method described will contribute for coding frame detection in uncharacterized DNA sequences such as it is the case in shotgun metagenomics, for instance.
Nicolas Carels
Oswaldo Cruz Foundation
Read the Original
This page is a summary of: Universal Features for the Classification of Coding and Non-coding DNA Sequences, Bioinformatics and Biology Insights, January 2009, SAGE Publications,
DOI: 10.4137/bbi.s2236.
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