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Literature DB >> 10988018

Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences.

G Dodin¹, P Vandergheynst, P Levoir, C Cordier, L Marcourt.

Abstract

A correlation function that compares each base in a DNA sequence to its various neighbours and which is subsequently processed by Fourier and wavelet transforms has been developed. The procedure has been applied to sequences from the human chromosome 22, to nef genes from various HIV clones and to myosin heavy chain DNA. It permits to readily visualize regular features in DNA which are related to the stability of heteroduplexes formed upon strand slippage. Copyright 2000 Academic Press.

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Year: 2000 PMID： 10988018 DOI： 10.1006/jtbi.2000.2127

Source DB: PubMed Journal: J Theor Biol ISSN： 0022-5193 Impact factor: 2.691

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Cited

14 in total

1. A hybrid technique for the periodicity characterization of genomic sequence data.

Authors: Julien Epps
Journal: EURASIP J Bioinform Syst Biol Date: 2009-04-08

2. Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences.

Authors: Benjamin Audit; Cédric Vaillant; Alain Arnéodo; Yves d'Aubenton-Carafa; Claude Thermes
Journal: J Biol Phys Date: 2004-03 Impact factor: 1.365

3. Sequence periodic pattern of HERV LTRs: a matrix simulation algorithm.

Authors: Shihua Zhang; Jing Xu; Chaoling Wei
Journal: J Biosci Date: 2012-03 Impact factor: 1.826

4. Visualization of the protein-coding regions with a self adaptive spectral rotation approach.

Authors: Bo Chen; Ping Ji
Journal: Nucleic Acids Res Date: 2010-10-14 Impact factor: 16.971

5. Statistical methods for detecting periodic fragments in DNA sequence data.

Authors: Julien Epps; Hua Ying; Gavin A Huttley
Journal: Biol Direct Date: 2011-04-28 Impact factor: 4.540

6. Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.

Authors: Vladimir Paar; Nenad Pavin; Ivan Basar; Marija Rosandić; Matko Gluncić; Nils Paar
Journal: BMC Bioinformatics Date: 2008-11-03 Impact factor: 3.169

Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences.

1. A hybrid technique for the periodicity characterization of genomic sequence data.

2. Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences.

3. Sequence periodic pattern of HERV LTRs: a matrix simulation algorithm.

4. Visualization of the protein-coding regions with a self adaptive spectral rotation approach.

5. Statistical methods for detecting periodic fragments in DNA sequence data.

6. Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.

7. The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.

8. Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements.

9. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance.

10. Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.