Search of hidden periodicities in DNA sequences

Chechetkin, V. R.; Turygin, A. Yu.

doi:10.1006/jtbi.1995.0155

Cited by 51 publications

(53 citation statements)

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Order and correlations in genomic DNA sequences. The spectral approach

Lobzin¹,

Chechetkin²

2000

Usp. Fiz. Nauk

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Order and correlations in genomic DNA sequences. The spectral approach

Lobzin¹,

Chechetkin²

2000

Usp. Fiz. Nauk

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“…We are motivated from the fact that in many cases the usual aforementioned techniques do not seem to be adequate for detecting hidden periodicities on symbolic sequences (see [3]), so we build a new method for detecting periodicities presented in sections 2 and 3. Downloaded by [Selcuk Universitesi] at 18:57 08 January 2015…”

Section: Introductionmentioning

confidence: 99%

Detecting hidden periodicities on symbolic sequences

Atreas

2009

Journal of Interdisciplinary Mathematics

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“…MacLachlan and Stewart used Fourier transforms to find a 14-fold periodicity in α-tropomysin, and demonstrated the statistical significance of this result through a mathematical analysis of the Fourier transform method [2] ; the 14-fold periodicity was later confirmed by X-ray crystallography [3 ; 4]. Statistically significant periodicities have also been found through the application of Fourier transform methods to DNA sequences [5][6][7][8]. At a more local level of protein structure, Fourier transforms have been successfully applied in conjunction with hydrophobicity scales to reveal amphiphilic secondary structures in protein sequences [9][10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Criteria for confirming sequence periodicity identified by Fourier transform analysis: Application to GCR2, a candidate plant GPCR?

Illingworth

Parkes²,

Snell³

et al. 2008

Biophysical Chemistry

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. Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR?. Biophysical Chemistry, Elsevier, 2008, 133 (1-3) This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT2 AbstractMethods to determine peridiodicity in protein sequences are useful for inferring function. Fourier transformation is one approach but care is required to ensure the periodicity is genuine. Here we have shown that empirically-derived statistical tables can be used as a measure of significance.Genuine protein sequences data rather than randomly generated sequences were used as the statistical backdrop. The method has been applied to G-protein coupled receptor (GPCR) sequences, by Fourier transformation of hydrophobicity values, codon frequencies and the extent of over-representation of codon pairs; the latter being related to translational step times. Genuine periodicity was observed in the hydrophobicity whereas the apparent periodicity (as inferred from previously reported measures) in the translation step times was not validated statistically. GCR2 has recently been proposed as the plant GPCR receptor for the hormone abscisic acid. It has homology to the Lanthionine synthetase C-like family of proteins, an observation confirmed by fold recognition. Application of the Fourier transform algorithm to the GCR2 family revealed strongly predicted seven fold periodicity in hydrophobicity, suggesting why GCR2 has been reported to be a GPCR, despite negative indications in most transmembrane prediction algorithms. The underlying multiple sequence alignment, also required for the Fourier transform analysis of periodicity, indicated that the hydrophobic regions around the 7 GXXG motifs commence near the C-terminal end of each of the 7 inner helices of the α-toroid and continue to the N-terminal region of the helix. The results clearly explain why GCR2 has been understandably but erroneously predicted to be a GPCR.

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Search of hidden periodicities in DNA sequences

Cited by 51 publications

References 0 publications

Order and correlations in genomic DNA sequences. The spectral approach

Order and correlations in genomic DNA sequences. The spectral approach

Detecting hidden periodicities on symbolic sequences

Criteria for confirming sequence periodicity identified by Fourier transform analysis: Application to GCR2, a candidate plant GPCR?

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