AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.

ABSTRACT: Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data fr

SUBMITTER: Ruiz-Ciancio D 

PROVIDER: S-EPMC10680646 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature