Seven Clusters in Genomic Triplet Distributions

Article type: Research Article

Authors: Gorban, Alexander N.^; | Zinovyev, Andrei Y. | Popova, Tatyana G.

Affiliations: Institute of Computational Modeling, Russian Academy of Science | Institute of Polymer Physics, ETH, Switzerland | Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette, France

Note: [] Corresponding author. E-mail: zinovyev@ihes.fr

Abstract: In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring a learning dataset of already known genes. The fact that unsupervised genedetection is possible is closely connected to the existence of a cluster structure in oligomer frequency distributions. In this paper we study the cluster structure of several genomes in the space of their triplet frequencies, using a pure data exploration strategy. Several complete genomic sequences were analyzed, using the visualization of tables of triplet frequencies in a sliding window. The distribution of 64-dimensional vectors of triplet frequencies displays a well-detectable cluster structure. The structure was found to consist of seven clusters, corresponding to proteincoding information in three possible phases in one of the two complementary strands and in the non-coding regions with high accuracy (higher than 90% on nucleotide level). Visualizing and understanding the structure allows to analyze effectively the performance of different gene-prediction tools. Since the method does not require extraction of ORFs, it can be applied even for unassembled genomes.

Keywords: visualization, gene recognition, unsupervised learning, codon usage

Journal: In Silico Biology, vol. 3, no. 4, pp. 471-482, 2003