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Table 4 Notations used in Table 3

From: A comparative study of conservation and variation scores

N No. of sequences in alignment.
A ik The amino acid in sequence i at alignment site k.
d(A i , A j ) Sequence distance in percent.
p k Probability estimated from site k.
p Probability estimated from alignment.
q Probability estimated from database.
S b (k)
R(p k , p)
V (p k ) -Tr(ω log20 ω), Tr(ω) = 1
ω = diag(p k 1), , p k 20)) × M f
n k No. of occurences in site k.
n No. of average occurences in a site.
α 0 (k) Most common amino acid at k.
d k No. of different amino acids at k.
M The BLOSUM62 matrix, containing log-odds ratios (blosum62.bla).
M f The BLOSUM62 matrix of frequencies (blosum62.qij ).
M V
M K
M M M f normalized such that each row and column approx. sums to 1.
M L M normalized such that M L (α, α) = 10; 2 ≤ M L (α, β) ≤ 10