Influence on maximal discrimination by choice of oligonucleotides used by W8 method. The W8 method normally uses all octanucleotide frequencies in its reference set. Here, the method was modified so that only the n% octanucleotides with the lowest frequencies were used, where n varied from 10 to 100. In all cases, the target genome was contaminated to a level of 3% by foreign genes. (A) A HIP1-rich genome (that of Syn; 47.4% GC, 855 HIP1/million nt) was contaminated with genes from a HIP1-rich genome (from Tel; 53.9% GC, 1418 HIP1/million nt). The bars show standard deviations from repetitions with three different sets of contaminating genes. (B) A low-GC, HIP1-poor (36.4% GC, 2 HIP1/million nt) genome (Pma) was contaminated with genes from the HIP1-poor genomes of either Pmt (♦; 50.7 GC%, 39 HIP1/million nt) or Cel (■; 35.4 GC%, 5 HIP1/million nt). A high-GC, HIP1-poor genome (Gvi; ▲; 62.0% GC, 68 HIP1/million nt) or HIP1-rich genome (Tel; ×; 53.9% ?GC, 1418 HIP1/million nt) was contaminated with high-GC genes from Syw (59.4% GC, 64 HIP1/million nt). The inset shows at the same scale the spike near 100% usage of the reference set with Tel as the target genome.
Elhai et al. BMC Genomics 2012 13:245 doi:10.1186/1471-2164-13-245