Table 3 Scoring methods at an alignment site k

I

Lockless99

S

Pei01var(w)

Stereochemical properties

I

Taylor86

min|{T _j :A _k ⊆ T _j }|, j = 1,...,61

I

Zvelebil87

0.9 - 0.1n _dis

Symbol entropy

S

Sander91

S₂₀(p _k )

S

Shenkin91

S

Gerstein95

S₂(p _k ) - S₂(p)

I

Wang06w

R(p _k , q)

I

Capra07w

(R(p _k , r) + R(q, r))/2, r = (p _k + q)/2

Stereochemically sensitive entropy

S

Mirny99

S _e (p _k ), AA = {AVLIMC, FWYH, STNQ, KR, DE, GP}

S

Williamson95

R(p _k , p), AA = {VLIM, FWY, ST, NQ, HKR, DE, AG, P, C}

S

Caffrey04w

V(p _k )

Substitution matrix

S

Sander91sp

I

Karlin96

S

Valdar01

S

Pei01sp(w)

I

Thompson97

I

Mihalek07

I

Liu08w

Phylogeny

S

Mihalek04

I

Zhang08

D

Mayrose04

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