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

• Main Authors: Nunes Miriam CS, Wanner Elizabeth F, Weber Gerald
• Format: Article
• Language: English
• Published: BMC 2011-12-01
• Series: BMC Genomics

<p>Abstract</p> <p>Background</p> <p>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 <it>k</it>/21 which were reported for a tiny section of chromosome 2 in <it>P. falciparum</it>? Are these present in other chromosomes and perhaps in related organisms? And how should we interpret fractional periodicities in genomes?</p> <p>Results</p> <p>We applied the binary indicator power spectrum to all chromosomes of <it>P. falciparum</it>, and found that the frequency overtones <it>k</it>/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.</p> <p>Conclusions</p> <p>Some authors hinted recently at the possibility of mapping artifacts and frequency aliases in power spectra. However, in the case of <it>P. falciparum</it> 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.</p>