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Table 3 Scoring methods at an alignment site k

From: A comparative study of conservation and variation scores

Symbol frequency S Wu70 d k /p k 0(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 Rate4Site
  1. Methods labeled as S: available in SEALA package at http://github.com/fredrikj, I: implemented for this study and available at http://github.com/fredrikj/bioruby, D: downloaded from the Rate4Site website http://consurf.tau.ac.il. Scores ending with "w" use sequence weighting by Henikoff and Henikoff [9]. Scores ending with "(w)" are used both with and without weights. Explanation of notations are given in Table 4, and further details can be found in the main text.