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Fig. 1 | BMC Bioinformatics

Fig. 1

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

Fig. 1

Automatic quality assessment method for PWM clustering. First, a similarity score matrix for PWMs in a cluster is calculated and Z-score is calculated for each row (one row represents one PWM; Z-scores of one PWM versus all others). Then, Z-scores less than a threshold (e.g., < − 1) are counted to make a frequency count vector, which is sorted and the top 15% of them (default parameter in abc4pwm) are selected as putative poorly clustered PWMs. Finally, the poorly clustered PWMs are identified and be removed from clusters (e.g., PWMs 15, 3, 20 and 21 in the figure)

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BMC Bioinformatics

ISSN: 1471-2105

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