Title :
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
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;
Conference_Titel :
Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on
Conference_Location :
Arlington, VA
Print_ISBN :
0-7695-0862-6
DOI :
10.1109/BIBE.2000.889603
