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. 2005 Jan 4;3(1):e10. doi: 10.1371/journal.pbio.0030010

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Copyright: © 2005 Sean R. Eddy.

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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One convenient threshold-independent measure of the strength of a comparative analysis is an expected Z score, the expected difference Δc in the number of substitutions in a neutral feature alignment versus a conserved feature alignment, normalized to units of standard deviations. E(Z) is readily calculated for the binomial distribution:

where p_n and p_c are the probabilities of observing a change at one aligned comparative nucleotide according to the Jukes-Cantor equation.

The plots here are for N = 5 and L = 8. The shape of the curve is independent of N and L, while the absolute magnitude of Z scales as √NL . The x-axis is shown from D = 0 to D = 4, beyond the more realistic range of Figures 1 and 2, to show the mathematically optimum D if homologous conserved features were present, recognized, and accurately aligned at any D.

graphic file with name pbio.0030010.e003.jpg — One convenient threshold-independent measure of the strength of a comparative analysis is an expected Z score, the expected difference Δc in the number of substitutions in a neutral feature alignment versus a conserved feature alignment, normalized to units of standard deviations. E(Z) is readily calculated for the binomial distribution:

where p_n and p_c are the probabilities of observing a change at one aligned comparative nucleotide according to the Jukes-Cantor equation.

The plots here are for N = 5 and L = 8. The shape of the curve is independent of N and L, while the absolute magnitude of Z scales as √NL . The x-axis is shown from D = 0 to D = 4, beyond the more realistic range of Figures 1 and 2, to show the mathematically optimum D if homologous conserved features were present, recognized, and accurately aligned at any D.