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 log_{20} ω), Tr(ω) = 1 ω = diag(p_{ k }(α_{1}), ⋯, p_{ k }(α_{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 |