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

Abstract

Aptamer; Bioinformatics; Sequence analysis

Aptàmer; Bioinformàtica; Anàlisi de seqüència

Aptámero; Bioinformática; Análisis de secuencia

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 aptamers with ranking data, such as fold enrichment or scoring algorithm results, represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner have broad-reaching implications for aptamer researchers across a wide range of disciplines.

This work was supported by an American Heart Association scientist development grant (14SDG18850071 to W.H.T.), the National Institutes of Health (R01HL139581 and R01HL157956 to W.H.T.; K22CA263783 to K.W.T.), the National Science Foundation (IIS-1817239 to R.S.), the Department of Defense (DOD CDMRP-PRCRP CA220729 to K.W.T.), the American Cancer Society (HCCC, IRG-18-165-43 to S.V.), the Bunge and Born Fund (FBB-20170609 to D.R.C.), and the Fulbright-Argentinean Ministry of Education (ME-FLB-2022-2023 to D.R.C.).