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We won on the Thursday, and on the Sunday we met to select positions, and somebody said... Shall I tell you who? Yes, I will: it was Chris Smith [later culture secretary in the Blair government].
Think of it as practice: It allows us to begin to recognize commonalities about the positions that interest us, eventually helping us select positions to pursue.
We randomly select positions and velocities for N equal mass stars from the virialised Plummer distribution (Plummer 1911), for (N=2, 4, 8), …, up to 1,024.
We select positions such that P < 5 × 10−9 in the case sample but no 100-bp STR occurrences are present in any of the control samples.
If the gene does not have an annotated stop codon, we select positions from the last 500 nt but not including the last 100 nt upstream of the mode of the PAS.
A custom Perl script (Additional File 1) was developed to select positions where only one parent was polymorphic so that progenies would be heterozygous in a 1 1 ratio.
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The Bayesian random-effects method detected ten positively selected positions with very high confidence (posterior probability >95%) and another four with less confidence (posterior probability 90 95%) (Table 4).
Mutation experiments of D1 protein will unveil the functional importance of the positively selected positions.
The positively selected positions were compared to the human Swiss-Prot sequence (Q15831).
Both models identified 4 codons (codons number 7, 9 25 and 27) under strong positive selection, and a number of less strongly selected positions (Figure 3).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com