A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data

The exponential growth of genome sequences available has spurred research on pattern detection with the aim of extracting evolutionary signal. Traditional approaches, such as multiple sequence alignment, rely on positional homology in order to reconstruct the phylogenetic history of taxa. Yet, mining information from the plethora of biological data and delineating species on a genetic basis, still proves to be an extremely difficult problem to consider. Multiple algorithms and techniques have been developed in order to approach the problem multidimensionally. Here, we propose a computational framework for identifying potentially meaningful features based on k-mers retrieved from unaligned sequence data. Specifically, we have developed a process which makes use of unsupervised learning techniques in order to identify characteristic k-mers of the input dataset across a range of different k-values and within a reasonable time frame. We use these k-mers as features for clustering the input sequences and identifying differences between the distributions of k-mers across the dataset. The developed algorithm is part of an innovative and much promising approach both to the problem of grouping sequence data based on their inherent characteristic features, as well as for the study of changes in the distributions of k-mers, as the k-value is fluctuating within a range of values. Our framework is fully developed in Python language as an open source software licensed under the MIT License, and is freely available at https://github.com/BiodataAnalysisGroup/kmerAnalyzer.