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Table 1 The definitions of six metrics used for motif comparison.

From: SPIC: A novel similarity metric for comparing transcription factor binding site motifs based on information contents

Similarity metric Formula References
Average log-likelihood ratio (ALLR) A L L R ( X , Y ) = b N X b Y b q b + b N Y b X b q b b ( N X b + N Y b ) Wang and Stormo [18]
Average Kullback-Leibler ( AKL) A K L ( X , Y ) = 10 - b X b log X b Y b + b Y b log Y b X b 2 Kullback and Leibler [19]
Sum of squared distances (SSD) S S D ( X , Y ) = 2 - b ( X b - Y b ) 2 Schones et al. [17]
1-p-value of Chi-square (pCS) χ 2 ( X , Y ) = b ( N X b - N X b e ) 2 N X b e + b ( N Y b - N Y b e ) 2 N Y b e Schones et al. [17]
Pearson correlation coefficient ( PCC) P C C ( X , Y ) = b ( X b - X ¯ ) ( Y b - Y ¯ ) b ( X b - X ¯ ) 2 b ( Y b - Y ¯ ) 2 Pietrokovski [20]
Asymptotic Covariance (AC) A C ( A , B ) = lim m m - 1 cov ( N A ( m ) + N A ( m ) , N B ( m ) + N B ( m ) ) Pape et al. [24]