Distance Analysis of Min Max Normalized Score Vs Old Normalized Score

We present the comparisons of min max normalized score distances vs old normalized score distances for the COG consensus data set.

Min Max Normalized Score (MMNORM) = (score - min) / (max - min) where,
max = Max(AA, BB) and
min = 2*GO + (Alen + Blen)*GE for Needleman-Wunsch or 0 for Smith-Waterman

Old Normalized Score = 2*AB/(AA + BB)

Note. XY is the score when sequence X is aligned with sequence Y.
Note. Xlen is the length of sequence X.
Note. GO is gap open and GE is gap extension penalties

Index

• Needleman-Wunsch Min Max Normalized Score (MMNORM) Vs Old Normalized Score (OLDNORM)
  

  BLOSUM62

  |

  Position Specific Scoring Matrix

• Needleman-Wunsch Min Max Normalized Score (MMNORM) Vs Old Normalized Score (OLDNORM) [Top]



BLOSUM62	Position Specific Scoring Matrix