Improved functions for non-linear sequence comparison using SEEKR

Abstract

SEquence Evaluation through k-mer Representation (SEEKR) is a method of sequence comparison that utilizes sequence substrings called k-mers to quantify non-linear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate p values that ascribe statistical significance to SEEKR-derived similarities as well as visualize different aspects of k-mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that contain XIST-like sequence features and demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and outline the best practice of visualizing RNA-Seq read density to evaluate support for lncRNA annotations prior to their in-depth study in cell types of interest.