Improved functions for nonlinear sequence comparison using SEEKR.

SEquence Evaluation through -mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings called -mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects of -mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that contain -like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains.

Improved functions for non-linear sequence comparison using SEEKR.

SEquence Evaluation through -mer Representation (SEEKR) is a method of sequence comparison that utilizes sequence substrings called -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 -mer similarity. We apply the new functions to identify chromatin-enriched long noncoding RNAs (lncRNAs) that harbor -like sequence fragments and show that several of these fragments are bound by -associated proteins.