Table 1

Change in maximal discrimination by W8 method in response to range of reference seta
Source of contaminationb
High GC Low GC
High HIP1 High 8mer Low 8mer High HIP1 High 8mer Low 8mer
Targetb
    High CG
High HIP1 +0.30 (2) –0.47 (3) –0.03 (3) +0.15 (9) (0) (0)
High 8mer –0.01 (3) –0.13 (6) –0.02 (3) (0) (0) (0)
Low 8mer +0.21 (4) –0.05 (2) +0.07 (3) +0.04 (8) –0.02 (2) –0.06 (0)
    Low CG
High HIP1 +0.30 (8) –0.07 (7) –0.04 (8) +0.12 (21) +0.04 (8) –0.04 (2)
High 8mer (0) (0) –0.02 (1) +0.07 (10) +0.04 (3) +0.09 (0)
Low 8mer (0) (0) (0) (0) (0) (0)

a The values shown are the compilation of results of 116 experiments in which genes taken at random from one genome were used to contaminate a target genome (see Methods for further explanation and Additional file 2 (Table  1) for a listing of the data on which the table is based). Each value shown is the difference of the maximal discrimination calculated using the W8 method subtracted from the value calculated using a modified W8 method in which the 40% least frequent octanucleotides were chosen as the reference set. Values in which the difference is at least 5 percentage points in favor of the 40% choice of octamers are rendered in bold. Those in which the difference is at least 5 percentage points in favor of the 100% choice of octamers are rendered in bold italics.

b The categories of the source/target combinations were determined by whether the source and target genomes were high GC (> 50%) or low and by the frequency of the most frequent octameric sequence: high HIP1 if the most frequent octamer is GCGATCGC (HIP1) and occurs at least 180 instances per million nucleotides, high 8mer if the most frequent octamer is not HIP1 and occurs at least 180 instances per million nucleotides, and otherwise low 8mer. The number in parentheses indicates the number of times the particular source/target combination was tested. Combinations were counted only if at least one condition (40% or 100% oligomers in reference set) yielded a maximal discrimination value between 0.10 and 0.90.

Elhai et al.

Elhai et al. BMC Genomics 2012 13:245   doi:10.1186/1471-2164-13-245

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