Improved Python Package for DNA Sequence Encoding using Frequency Chaos Game Representation

Abstract

SummaryFrequency Chaos Game Representation (FCGR), an extended version of Chaos Game Representation (CGR), emerges as a robust strategy for DNA sequence encoding. The core principle of the CGR algorithm involves mapping a onedimensional sequence representation into a higher-dimensional space, typically in the two-dimensional spatial domain. This paper introduces a use case wherein FCGR serves as a kmer frequency-based encoding method for motif classification using a publicly available dataset. Availability and implementationThe FCGR python package, use case, along with additional functionalities, is available in the GitHub. Our FCGR package demonstrates superior accuracy and computational efficiency compared to a leading R-based FCGR library [1], which is designed for versatile tasks, including proteins, letters, and amino acids with user-defined resolution. Nevertheless, it is important to note that our Python package is specifically designed for DNA sequence encoding, where the resolution is predetermined based on the kmer length. It is a drawback of our current package compared to the state-of-the-art R-based kaos package [1].