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Figure 1 | BMC Genomics

Figure 1

From: Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

Figure 1

Results of MIC/MAC comparative genomic hybridization. A: Distribution of MIC scaffold ratios. Red line: proposed separation of MAC-destined (maD) DNA scaffolds (on the left) and MIC-limited (miL) scaffolds (on the right). B: Scatter plot of MIC scaffold ratios as a function of scaffold length. Pink and aqua points: maD and miL DNA, respectively, by the log2 ratio criterion in Figure 1A. Black diamonds and small black circles, respectively: miL and maD scaffolds with high sequence identity to miL transposon genes. The maD distribution is more diffuse as the length decreases to the minimum scaffold length (1,000 bp). This is attributed to the fact that the number of probes is roughly proportional to scaffold length. Given a uniform intrinsic variability in hybridization ratios for each probe, the variance of the scaffold means is expected to vary inversely with scaffold length. The secondary peak in the maD distribution (around log2 ratio = -0.45) in 1A and the multimodality of the maD distribution in 1B (most clearly seen for scaffolds > 50 kb) are caused by the partial loss of MIC chromosome segments in the cells used for the MIC DNA preps (Orias and Hamilton, unpublished observations).

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