Related Experiment Video
Updated: Aug 26, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Seven clusters in genomic triplet distributions
Alexander N Gorban1, Andrei Y Zinovyev, Tatyana G Popova
1Institute of Computational Modeling, Russian Academy of Science.
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 gene-detection 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 protein-coding 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.
Related Concept Videos
Karyotyping
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule
Single Nucleotide Polymorphisms-SNPs
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
¹H NMR Signal Multiplicity: Splitting Patterns

