A simple and species-independent coding measure.
We present a coding measure which is based on the statistical properties of the stop codons, and that is able to estimate accurately the variation of coding content along an anonymous sequence. As the stop codons play the same role in all the genomes (with very few exceptions) the measure turns out to be species-independent. We show results both for prokaryotic and for eukaryotic genomes, indicating, first, the accuracy of the measure, and, second, that better prediction is achieved if the measure is applied on homogeneous, isochore-like sequences than if it is applied following the standard moving window approach. Finally, we discuss on some of the possible applications of the measure.
Carpena
P
P
Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, Malaga, Spain. pcarpena@ctima.uma.es
Bernaola-Galván
P
P
Román-Roldán
R
R
Oliver
J L
JL
D000818:Animals; D001412:Bacillus subtilis / Q000235:genetics; D001482:Base Composition; D018388:Codon, Terminator / Q000235:genetics*; D030561:Databases, Nucleic Acid; D004331:Drosophila melanogaster / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D032085:Isochores / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D013045:Species Specificity; D013223:Statistics as Topic
D018388:Codon, Terminator; D032085:Isochores