Evolution of biosequence search algorithms: a brief survey

TL;DR

This survey reviews the evolution of biosequence search algorithms, highlighting shifts from alignment-based to alignment-free and sketching methods driven by technological advances and data growth.

Contribution

It provides a comprehensive overview of key algorithmic developments in biological sequence comparison, emphasizing recent trends and future challenges.

Findings

Shift from alignment-based to alignment-free methods

Emergence of sketching techniques for large datasets

Focus on algorithmic challenges in population genomics

Abstract

The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm, advent of new sequencing technologies, and a substantial increase in size of the available data. We discuss the expansion of alignment-free techniques coming to replace alignment-based algorithms in large-scale analyses. We further emphasize recently emerged and growing applications of sketching methods which support comparison of massive datasets, such as metagenomics samples. Finally, we focus on the transition to population genomics and outline associated algorithmic challenges.