Genomic signature using FCGR

Genomic signature using FCGR transforms genomic oligonucleotide frequencies into frequency chaos game representation (FCGR/CGR) images to characterize DNA structural patterns for sequence classification and phylogenetic distance measurement.

Key Features:

• Chaos Game Representation (CGR/FCGR): Converts oligonucleotide frequency counts into two-dimensional images that represent sequence composition and spatial distribution of k-mers.
• Genomic Signature Concept: Encodes subsequence-derived features such as base concentrations, stretches (runs of complementary bases or purines/pyrimidines), and patches (over- or underrepresented words) that reflect genome-wide signatures.
• Phylogenetic Analysis: Assesses phylogenetic proximity by measuring distances between CGR/FCGR images of different genomes.
• Classification of Organisms: Distinguishes eukaryotic and prokaryotic organisms based on DNA structural patterns captured in FCGR images.

Scientific Applications:

• Genomic Research: Visualizes oligonucleotide distributions to identify structural features relevant to genomics and molecular biology.
• Evolutionary Biology: Enables comparison of phylogenetic relationships by using FCGR image differences to infer genetic proximity.
• Taxonomy: Provides a sequence-based method to classify organisms, including separation of eukaryotes and prokaryotes, using DNA structural signatures.

Methodology:

Maps nucleotides onto a two-dimensional plane and transforms oligonucleotide frequency counts into FCGR/CGR images where each point represents specific subsequences, and the resulting images reflect local and global distributional features of the genome.