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Figure 5 | BMC Bioinformatics

Figure 5

From: Improving the specificity of high-throughput ortholog prediction

Figure 5

Ortholuge R1 × R2 plots (Ratio1 versus Ratio2) for selected eukaryotic data, where each point represents one putative ortholog group. (A) Putative orthologous groups identified using RBH for mouse-rat-human (Figure 4 shows the corresponding histogram). (B) Putative orthologs groups for mouse-rat-human from a higher quality (more precise) dataset (see Methods). It is expected that this more precise data set comprises primarily true orthologs. (C) A lower quality data set of RBH-predicted orthologous groups for cattle-human-mouse, where cattle genes have been identified from an incomplete genome sequence. (D), (E), (F) are zoomed-in versions of (A), (B), (C), respectively, with axes shown from 0 to 2 instead of 0 to 30. Note that most orthologous groups exhibit low Ratio1 and Ratio2 values, in all three data sets. For example, in panels A and D, about 86% of orthologs have Ratio1 and Ratio2 values less than 1. However, the higher quality data set (panels B and E) contains fewer points at higher Ratio values versus the RBH-predicted data set. The lower quality data set contains more points with very high Ratio2 values (i.e. only 73% of points have Ratio1 and Ratio2 values less than 1), potentially reflecting the increased occurrence of probable cattle paralogs (i.e. paralogs being misidentified as orthologs by an RBH-analysis with an incomplete cattle genome).

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