Title: Aptamer Clustering using Mapper

Abstract: Aptamers are RNA molecules that can bind to a specific target, like antibodies, but are up to 20 times smaller and are chemically synthesized. Aptamer research ponders these molecules and searches for causes of aptamers binding or not binding to desired target molecules, as well as methods to construct new aptamers. A natural place to start is to cluster together groups of aptamers which bind to similar or different targets, and then look for similarities or differences between those aptamers. We use the Mapper algorithm from topological data analysis to investigate the reverse problem — do aptamers with genetic or structural similarities bind to similar targets, and do aptamers with significant genetic or structural differences bind to different targets?