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Table 2 Biological meaning of WordCluster predictions*

From: WordCluster: detecting clusters of DNA words and genomic elements

Method

#islands

#TSS overlap

#R13 overlap

#Alu overlap

#PhastCons overlap

cpg50

198703

12432 (6.3%)

30660 (15.4%)

80323 (40.4%)

48787 (24.6%)

cpgISc

194724

11926 (6.1%)

34567 (17.8%)

70144 (36.0%)

48930 (25.1%)

cpgISg

204238

12156 (6.0%)

37616 (18.4%)

70456 (34.5%)

52335 (25.6%)

  1. *Comparison of three WordCluster predictions of CG clusters (CpG islands) using three different distance models: cpgISg (genome intersection), cpg50 (median) and cpgISc (chromosome intersection). The overlap with two gene regions (TSS and R13), Alu elements and phylogenetically conserved PhastCons elements have been measured and both absolute numbers and percentages are given.
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Algorithms for Molecular Biology

ISSN: 1748-7188