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In MIp, a term called average product correction (APC) is subtracted from the MI score for each pair of positions in order to reduce false positives.
For each pair of positions i and j, 300 randomized coevolution measures (for MI, MI/Hi,j, and Res) were calculated by randomly mixing the amino acids across the sequences of the MSA that were not gapped at either.
The computed MI values are displayed on a 2D grid plot displaying the ordered pair of positions (j,k) on the vertical and horizontal axis respectively (only pairs with j
A pair of positions (M, N) in aligned sequences, each of which has two nucleotides (m1 and m2 in position M, n1 and n2 in position N), may have three possible combinations (Fig. 6a), (i) four alleles (m1n1, m1n2, m2n1, m2n2), (ii) three alleles (one allele missing from i), (iii) two alleles (m1n1, m2n2).
One entry is calculated for each corresponding pair of positions.
And this for each pair of positions studied.
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The group's arguments are available in a pair of position papers — a briefing [pdf] and a memo [Word document] — written by Patrick Markee, the senior policy analyst there.
For methods using two ICAs, the average correlation was calculated for all possible combinations of pairs of ICAs (32 possible combinations for each pair of position indices evaluated).
Then, the pair of position and origin vectors for one of the resulting recombinant chromosomes is {[0, 12, 32, 47], [a, b, c, d]}.
Assuming a crossover occurs at base pair position 47 (e.g., 47.0 Mb), the pair of position and origin vectors for one of the resulting recombinant chromosomes is {[0, 47], [c, d]}.
During meiosis, assuming a crossover occurs at base pair position 12 (e.g., 12.0 Mb), the pair of position and origin vectors for one of the resulting recombinant chromosomes is {[0, 12], [a, b]}.
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