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 (α1), ⋯, p k (α20)) × 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 |
