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Literature DB >> 17037959

Wavelet analysis of DNA walks.

Adrian D Haimovich¹, Bruce Byrne, Ramakrishna Ramaswamy, William J Welsh.

Abstract

A wavelet transform of the DNA "walk" constructed from a genomic sequence offers a direct visualization of short and long-range patterns in nucleotide sequences. We study sequences that encode diverse biological functions, taken from a variety of genomes. Pattern irregularities in the transform are frequently associated with sequences of biological interest. Exonic regions, for example, visualize differently under wavelet analysis than introns, and ribosomal RNA regions display distinct universal signatures. DNA walk wavelet analysis can provide a sensitive and rapid assessment of the putative biological significance of genomic DNA.

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Year: 2006 PMID： 17037959 DOI： 10.1089/cmb.2006.13.1289

Source DB: PubMed Journal: J Comput Biol ISSN： 1066-5277 Impact factor: 1.479

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Cited

11 in total

1. Nonlinear analysis of tRNAs nucleotide sequences by random walks: randomness and order in the primitive informational polymers.

Authors: G Bianciardi; L Borruso
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2. Global self-regulation of the cellular metabolic structure.

Authors: Ildefonso M De la Fuente; Fernando Vadillo; Alberto Luís Pérez-Samartín; Martín-Blas Pérez-Pinilla; Joseba Bidaurrazaga; Antonio Vera-López
Journal: PLoS One Date: 2010-03-02 Impact factor: 3.240

Review 3. Quantitative analysis of cellular metabolic dissipative, self-organized structures.

Authors: Ildefonso Martínez de la Fuente
Journal: Int J Mol Sci Date: 2010-09-27 Impact factor: 5.923

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. Characterizing exons and introns by regularity of nucleotide strings.

Authors: Tonya Woods; Thanawadee Preeprem; Kichun Lee; Woojin Chang; Brani Vidakovic
Journal: Biol Direct Date: 2016-02-08 Impact factor: 4.540

6. Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics.

Authors: Suping Deng; Yixiang Shi; Liyun Yuan; Yixue Li; Guohui Ding
Journal: BMC Genomics Date: 2012-12-17 Impact factor: 3.969

Wavelet analysis of DNA walks.

1. Nonlinear analysis of tRNAs nucleotide sequences by random walks: randomness and order in the primitive informational polymers.

2. Global self-regulation of the cellular metabolic structure.

Review 3. Quantitative analysis of cellular metabolic dissipative, self-organized structures.

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

5. Characterizing exons and introns by regularity of nucleotide strings.

6. Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics.

7. Global self-organization of the cellular metabolic structure.

8. On the dynamics of the adenylate energy system: homeorhesis vs homeostasis.

9. Application of discrete wavelet transform for analysis of genomic sequences of Mycobacterium tuberculosis.

10. Wavelet analysis of DNA walks on the human and chimpanzee MAGE/CSAG-palindromes.