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. 2006 Aug 29;4(9):e286. doi: 10.1371/journal.pbio.0040286

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© 2006 Eisen et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Effective number of codons (ENc; a measure of overall codon bias) for each predicted ORF is plotted versus GC3 (the fraction of codons that are synonymous at the third codon position that have either a guanine or a cytosine at that position). The upper limit of expected bias based on GC3 alone is represented by the black curve; most T. thermophila ORFs cluster below the curve [red dots as in (B)].

(B) Principal component analysis of relative synonymous codon usage in T. thermophila. The 232 genes in the tail of the comma-shaped distribution (those with the most biased codon usage) are colored red.

(C) Principal component analysis of relative synonymous codon usage in P. falciparum.