Figure 2.

Characterizing functional satellite sequence features. Centromere sequence features associated with CENP-A ChIP sequences. (A) Reads were initially mapped to canFam2.0 and characterized relative to sequence classification, as indicated in pie graph. (B) Both CarSat1 and CarSat2 are highly enriched in the CENP-A ChIPseq dataset (pā€‰<ā€‰0.01) relative to genomic background estimates (as demonstrated by red dotted line). Other satellite families showed no evidence of enrichment and are combined into one data point. (C) CarSat satellite families (CarSat1 and CarSat2) show enrichment of select sequences in the CENP-A ChIP dataset on an xy-plot of two replicate enrichment estimates (log transformed relative enrichment scores), highlighting in red in the upper right quadrant those k-mers that are enriched in both comparisons as delineated with grey dotted lines. (D) CarSat k-mers that are enriched (red) compared to those that are not enriched (black), as a function of their observed frequency in the genome. Both high-copy and low-copy number k-mers are enriched in both satellite families.

Hayden and Willard BMC Genomics 2012 13:324   doi:10.1186/1471-2164-13-324
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