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. Here we present AptamerRunner, an aptamer sequence and/or structure clustering algorithm that synergistically integrates computational analysis with visualization and expertise-directed decision making. The visual integration of networked aptame

SUBMITTER: Ruiz-Ciancio D 

PROVIDER: S-EPMC11539416 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature