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Table 3 Comparison of top 7 performing alignment strategies of SPIC with the best strategies of existing methods for motif retrieval on Dataset-1.

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

  Accuracy
Strategy ZF PFMs(25) Non-ZF PFMs(71) Total(96)
SPIC/SW(gap open = 1.00) 0.620 0.921 0.841
SPIC/SW(gap open = 0.75) 0.613 0.918 0.837
SPIC/SW(gap open = 0.50) 0.614 0.916 0.837
SPIC/SW(gap open = 1.50) 0.605 0.916 0.835
SPIC/SW(gap open = 0.25) 0.606 0.915 0.835
SPIC/SW(ungapped) 0.610 0.916 0.836
SPIC/NW(gap open = 1.0) 0.585 0.793 0.731
KFV(4-mer, cosine angle) 0.600 0.915 0.833
PCC/SWU 0.600 0.887 0.813
SSD/SW 0.560 0.859 0.781
  1. The last three columns are the results for the zinc-finger (ZF), non-ZF, and total families, respectively. The performances of SSD/SW and PCC/SWU are quoted from the STAMP [11]. The data of KFV are quoted from [25]. Gap extension is equal to half the gap open.