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Table 1 A comparison of PWM clusters between abc4pwm and STAMP

From: abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis

DBD family

PWMs in DBD

Abc4pwm

STAMP

RHR

20

All good (3)

All good (3)

bHSH

27

All good (4)

1 mix 3 good (4)

T_box

32

All good (6)

All good (5)

Tryptophan

95

All good (12)

2 bad 1 mix 7 good (10)

HMG

101

10 good 1 mix (11)

2 bad, 9 good (11)

C2H2_ZF

161

5 bad 7 mix 12 good (24)

9 bad 3 mix 6 good (18)

  1. Here, results of a manual comparison of clustering quality between abc4pwm and STAMP are provided. Good = more than 90% of the PWMs in a cluster are identical, Mix = 70% of the PWMs in a cluster are similar, and Bad = less than 30% of the PWMs in a cluster are similar. Total number of clusters in each DBD family are shown in the parenthesis
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BMC Bioinformatics

ISSN: 1471-2105

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