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Table 6 Comparing Marina and F-MATCH given catalogs of PWMs and DNA motifs

From: Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites

Group size

PWMs (x 80)

DNA motifs (x 1,160)

(# sequences)

F-MATCH

Marina

F-MATCH

Marina

600

44

47

N/A

24

1500

0

50

N/A

41

2500

0

53

N/A

44

  1. A collection of 80 plant-specific PWMs were supplied to Marina. When group-sizes are relatively small and PWMs are used, both Marina and F-MATCH identify approximately the same number of over-represented TFBSs. However as group-sizes increased, Marina consistently identifies over-represented TFBSs. Marina also accepts DNA motifs if PWMs are not available; F-MATCH does not accept such models.
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Plant Methods

ISSN: 1746-4811