Genomic signature is preserved in short DNA fragments

Author

Deschavanne, Patrick ; Giron, Alain ; Vilain, Joseph ; Dufraigne, Christine ; Fertil, Bernard

Author_Institution

Inst. Nat. de la Sante et de la Recherche Med., Paris, France

fYear

2000

fDate

2000

Firstpage

161

Lastpage

167

Abstract

The “chaos game representation” (CGR) paradigm has been implemented to display the use of short oligonucleotides in genomes in the form of fractal images. These images can be considered as a genomic signature. Using an unsupervised classification approach, it is shown that short fragments of genomic sequences retain most of the characteristics of the species they come from. It thus appears possible to perform a global comparison of species by means of genome fragments found in databases. The efficiency of this approach is evaluated as a function of the size of the fragments and the length of the oligonucleotides

Keywords

DNA; biocybernetics; biology computing; chaos; fractals; game theory; genetics; pattern classification; unsupervised learning; chaos game representation; efficiency; fractal images; genome databases; genome fragments; genomic signature preservation; global species comparison; oligonucleotide length; short DNA fragments; species characteristics; unsupervised classification; Bioinformatics; Chaos; DNA; Displays; Fractals; Frequency; Genomics; Image databases; Lead compounds; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on

Conference_Location

Arlington, VA

Print_ISBN

0-7695-0862-6

Type

conf

DOI

10.1109/BIBE.2000.889603

Filename

889603