Abstract
Loop-seq is a pioneering high-throughput assay that enables the simultaneous quantification of intrinsic cyclizability across a large set of DNA fragments. However, the assay's reliance on biotin-tethered elongated DNA fragments introduces a tethering effect, leading to biased cyclizability measurements. We demonstrate that the current de-biasing technique is inadequate for fully mitigating this bias. To address this, we introduce DNAcycP2, an enhanced software tool that extends the capabilities of our previous platform, DNAcycP. DNAcycP2 incorporates a novel data augmentation approach to more effectively eliminate biotin tether bias, yielding more accurate estimates of intrinsic DNA cyclizability. Additionally, DNAcycP2 offers improved computational efficiency and expands accessibility through a newly developed R package alongside its existing Python package and web server, ensuring broader utility for the research community.