Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome

Nunes, Mirian C.S., Wanner, Elizabeth F. and Weber, Gerald (2011). Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome. BMC Genomics, 12 (4),

Abstract

Background: Fourier transforms and their associated power spectra are used for detecting periodicities and protein-coding genes and is generally regarded as a well established technique. Many of the periodicities which have been found with this method are quite well understood such as the periodicity of 3 nt which is associated to codon usage. But what is the origin of the peculiar frequency multiples k/21 which were reported for a tiny section of chromosome 2 in P. falciparum? Are these present in other chromosomes and perhaps in related organisms? And how should we interpret fractional periodicities in genomes? Results: We applied the binary indicator power spectrum to all chromosomes of P. falciparum, and found that the frequency overtones k/21 are present only in non-coding sections. We did not find such frequency overtones in any other related genomes. Furthermore, the frequency overtones were identified as artifacts of the way the genome is encoded into a numerical sequence, that is, they are frequency aliases. By choosing a different way to encode the sequence the overtones do not appear. In view of these results, we revisited early applications of this technique to proteins where frequency overtones were reported. Conclusions: Some authors hinted recently at the possibility of mapping artifacts and frequency aliases in power spectra. However, in the case of P. falciparum the frequency aliases are particularly strong and can mask the 1/3 frequency which is used for gene detecting. This shows that albeit being a well known technique, with a long history of application in proteins, few researchers seem to be aware of the problems represented by frequency aliases.

Publication DOI: https://doi.org/10.1186/1471-2164-12-S4-S4
Divisions: Engineering & Applied Sciences
Additional Information: © 2011 Nunes et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article has been published as part of BMC Genomics Volume 12 Supplement 4, 2011: Proceedings of the 6th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (Xmeeting 2010). The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/12?issue=S4
Published Date: 2011-12-22
Authors: Nunes, Mirian C.S.
Wanner, Elizabeth F. ( 0000-0001-6450-3043)
Weber, Gerald

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