Evolution of biosequence search algorithms: a brief survey [article]

Gregory Kucherov
2018 arXiv   pre-print
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
more » ... d 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.
arXiv:1808.01038v4 fatcat:uiyjrwvgprgu3nfcu6i47o4wpe