APV-Sankey: a k-mer persistence visualization tool for HT-SELEX data analysis to identify aptamer candidates.

APV-Sankey is a novel visualization and analysis tool for High-Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX) data. By tracking k-mer persistence and concatenation across SELEX rounds via Sankey diagrams, APV-Sankey provides a complementary framework for identifying aptamer candidates, assessing SELEX progression, and facilitating the interpretation of HT-SELEX data. We demonstrate that k-mer persistence analysis captures biologically relevant patterns in SELEX evolution, complementing existing approaches based on sequence abundance. We benchmark APV-Sankey against standard metrics including final-round abundance, fold enrichment, and k-mer frequency, showing that persistence provides an orthogonal ranking dimension (Spearman ρ = - 0.192 with abundance) with 90% of top-200 persistent k-mers unique to the persistence ranking. APV-Sankey generates structured, round-annotated k-mer datasets suitable for downstream deep learning applications in aptamer binding prediction, positioning it as a data analysis platform for in silico aptamer research.