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Table 4 PMS5 on real datasets: predicting transcript factor-binding sites

From: PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem

Dataset

Best motif found by PMS5

Matched binding sites at:

mus05r

AGAGGAAAAAAAAAAGGAGAG

seq 1: GGAAAAACAAAGGTAATG

mus07r

GCTGCCCACCCTCTGCAACCC

seq 4: CCCAACACCTGCTGCCTGAGCC

mus11r

AGGGCGGGGGGCGGAGCGGGG

seq 2: GCCGCCGGGGTGGGGCTGAG

  

seq 3: GGGGGGGGGGGCGGGGC

  

seq 4: GTGGGGGCGGGGCCTT

  

seq 9: GAACAGGAAGTGAGGCGG

hm03r

AAAAGAAAAAAAAATAAACAA

seq 1: CGGGTGTTATTCAAGCAAAAAAAATAAATAAATACCTATGCAATAC

  

seq 2: GGATGTTACACAAGCAAACAAAATAAATATCTGTGCAATAT

  

seq 3: TGGGTGTTATATGAGCAAACAAAATAAATACCTGTGCAACAT

hm08r

CAGCGTGCAGTCCCCTTCATC

seq 10: TATGGTCATGACGTCTGACAGAGC

hm19r

CCCCCTTCCACCACCCACAGA

seq 2: CACTTTTAGCTCCTCCCCCCA

hm20r

CCTCCTTCCTCCCCCTCCCCC

seq 10: TCCTCCCCACCTTCCCCACCCTCCCCACCCTCCCCATAAGCGCCCCTCCCG

  

seq 11: GCAAACTCCGCCTCCCCCAA

  

seq 14: GTCCCTCCTCCTCCCGCCC

hm22r

GGACACGGCAGAGCCTGGGGA

seq 4: GAGGCAGACCACGTGAGAGCCTGGCCAGGCCTTCC

hm24r

CGCCTGCGCCCCGCCCCGCCC

seq 2: CCCCGCCCCGCGCTCCCC

hm26r

CCCCCCGCCTCCCGCTCCCAG

seq 3: CCCCGCCTCAGGCTCCCGGGG

  

seq 7: CTCAGCCTGCCCCTCCCAGGGATTAAG

  

seq 8: GCGCCGAGGCGTCCCCGAGGCGC