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bioRxiv · 10.1101/2024.03.10.584286

Improved functions for non-linear sequence comparison using SEEKR

Li, S.·Eberhard, Q.·Ni, L.·Calabrese, M.
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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 long noncoding RNAs (lncRNAs) that harbor XIST-like sequence fragments and show that several of these fragments are bound by XIST-associated proteins. We also highlight the best practice of using RNA-Seq data to evaluate support for lncRNA annotations prior to their in-depth study in cell types of interest.

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Li, S., Eberhard, Q., Ni, L., Calabrese, M.. 2024-03-10. Improved functions for non-linear sequence comparison using SEEKR. https://doi.org/10.1101/2024.03.10.584286

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