Elementolab/PBM Motifs

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  • Motif extraction. To extract motif number 1 from a PBM file called PFL1900wD1_pwm.txt, type: 
perl Bulyk_extract_pwm.pl PFL1900wD1_pwm.txt 1

Expected output: 

Created PBM_TTCTACAA_PFL1900wD1_pwm.txt with motif 1

Motif numbering is as specified in the PBM file. Some PBM files start with motif 0, others with motif 1


  • Entropy-based motif trimming. To trim a PBM motif by removing all side positions until an entropy < 1.25bits is reached, type: 
perl Bulyk_trim_pwm.pl PBM_TTCTACAA_PFL1900wD1_pwm.txt 1.25 1

Expected Output: 

Consensus = TCTACA
Created TPBM_TCTACA_PFL1900wD1_pwm.txt
Retrieved from "http://icb.med.cornell.edu/wiki/index.php/Elementolab/PBM_Motifs"
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