Cogprints

Application of The Method of Elastic Maps In Analysis of Genetic Texts

Gorban, Alexander N. and Zinovyev, Andrey Yu. and Wunsch, Donald C. (2003) Application of The Method of Elastic Maps In Analysis of Genetic Texts. [Conference Paper]

Full text available as:

[img]
Preview
PDF
1902Kb

Abstract

Abstract - Method of elastic maps ( http://cogprints.ecs.soton.ac.uk/archive/00003088/ and http://cogprints.ecs.soton.ac.uk/archive/00003919/ ) allows us to construct efficiently 1D, 2D and 3D non-linear approximations to the principal manifolds with different topology (piece of plane, sphere, torus etc.) and to project data onto it. We describe the idea of the method and demonstrate its applications in analysis of genetic sequences. The animated 3D-scatters are available on our web-site: http://www.ihes.fr/~zinovyev/7clusters/ We found the universal cluster structure of genetic sequences, and demonstrated the thin structure of these clusters for coding regions. This thin structure is related to different translational efficiency.

Item Type:Conference Paper
Keywords:SOM, Elastic net, Data modeling, Genome clusters, Genetic text, Translational efficiency
Subjects:Computer Science > Statistical Models
Computer Science > Artificial Intelligence
Biology > Theoretical Biology
ID Code:3961
Deposited By:Gorban, Prof Alexander N.
Deposited On:29 Nov 2004
Last Modified:11 Mar 2011 08:55

References in Article

Select the SEEK icon to attempt to find the referenced article. If it does not appear to be in cogprints you will be forwarded to the paracite service. Poorly formated references will probably not work.

[1] Gorban A.N., Pitenko A.A., Zinov'ev A.Y., Wunsch D.C. 2001. “Visualization of any data using elastic map method.” Smart Engineering System Design, V.11, p. 363-368.

[2] Gorban A.N., Zinovyev A.Yu. 2001. “Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology.” Institut des Hautes Études Scientifiques preprint. IHES/M/01/34, 2001

[http://www.ihes.fr/PREPRINTS/M01/Resu/resu-M01-34.html]

[3] Gorban A.N., Zinovyev A. Yu. Method of Elastic Maps and its Applications in Data Visualization and Data Modeling // International Journal of Computing Anticipatory Systems, CHAOS. 2001. V. 12. PP. 353-369.

[4] Fickett J.W. 1996. “The Gene Identification Problem: An Overview For Developers.” Computers Chem., Vol.20, No.1, pp.103-118.

[5] M. Gouy, Ch. Gautier. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Research, 10:7055-7070, 1982.

[6] I. Moszer, E.P.C. Rocha, A.Danchin. Codon usage and lateral gene transfer in Bacillus subtilis. Current Opinion in Microbiology, 2:524-528, 1999.

[7] P.M. Sharp, E. Cowe, D.G. Higgins, D.C. Shields, K.H. Wolfe, F.Wright. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity. Nucleic Acids Research, 16:8207-2811, 1988.

[8] C. Medigue, T. Rouxel, P. Vigier, A. Henaut, A. Danchin. Evidence for horizontal gene transfer in Escherichia coli speciation. Journal of Molecular Biology, 222:851-856, 1991.

Metadata

Repository Staff Only: item control page