Reconsidering the significance of genomic word frequencies.
By conventional wisdom, a feature that occurs too often or too rarely in a genome can indicate a functional element. To infer functionality from frequency, it is crucial to precisely characterize occurrences in randomly evolving DNA. We find that the frequency of oligonucleotides in a genomic sequence follows primarily a Pareto-lognormal distribution, which encapsulates lognormal and power-law features found across all known genomes. Such a distribution could be the result of completely random evolution by a copying process. Our characterization of the entire frequency distribution of genomic words opens a way to a more accurate reasoning about their over- and underrepresentation in genomic sequences.
Csurös
Miklós
M
Department of Computer Science and Operations Research, Université de Montréal, 8, succ. Centre-Ville, Montréal, Québec, Canada. csuros@iro.umontreal.ca
Noé
Laurent
L
Kucherov
Gregory
G
D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D023281:Genomics; D006801:Humans; D008390:Markov Chains; D009841:Oligonucleotides / Q000378:metabolism
D009841:Oligonucleotides