New SEEKR functions including those to estimate significance of k-mer similarity. (A) Console/command-line functions in SEEKR. Blue text, new or updated functions. Black text, retained functions. Orange text, deprecated functions. “seekr_filter_gencode” replaces “seekr_canonical_gencode.” “seekr_kmer_leiden” replaces “seekr_graph.” The “fasta-shuffle-letters” utility in the MEME Suite (Bailey et al. 2015) can be used in place of “seekr_gen_rand_rnas.” (B) Documentation of the Pearson's r-value threshold at a P-value of P = 0.05 for each probability distribution that best fits the list of r-values derived from 100,000 randomly selected pairwise comparisons from the set of GENCODE v43 Ensembl_canonical lncRNAs at k = 6. “Com.10 best fit”: pairwise comparisons fit to the common10 distributions in scipy.stats. “All best fit”: pairwise comparisons fit to all 124 probability distributions in scipy.stats. The Kolmogorov–Smirnov test was used to assess goodness-of-fit to each distribution. Fitting was repeated 10× for each of the common10 and all distributions. johnsonSU, Johnson's SU distribution. genhyperbolic, generalized hyperbolic distribution. (C) Number of lncRNAs detected as significant at the P < 0.05 threshold when fitting the set of background sequences to the common10 and at the specified subsetting sizes. (D) Number and identity of lncRNAs detected as significantly similar to XIST using k = 4, 5, or 6 when fit to a constant distribution (log-normal). (E) The SEEKR console commands used to download GENCODE lncRNAs and calculate adjusted P-values for a sequence comparison of interest. See also https://github.com/CalabreseLab/seekr2.0_update_manuscript.
