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Table 3 Discovered motifs using positive and negative data

From: A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements

Transcription factors Known motifs    WordSpy   MEME AlignACE
ACE2 CCAGCA GCTGG(1) CCAGC(2) GCTGGC(1) AACCAGC(2) AACCAGCA(7) AACCAGC(12)
Fkh1 GTAAACA GTAAACA(1) TGTTTAC(2) GTAAACAA(1) TTGTTTAC(2) GTAAACAA(1) AAANGTAAACA(5)
Fkh2 GTAAACA GTAAACA(1) TGTTTAC(2) GTAAACAA(1) TTGTTTAC(2) TTGTTTAC(1) AANRWAAACA(3)
Mbp1 ACGCGT ACGCGT(1) AACGCGT(1) ACGCGTT(2)   AACGCGTT(2) RACGCGWY(3)
  CRCGAAA GACGCGA(3) TCGCGTC(5) ACGCGAA(6)   n/a ACGCGWAAAA(9)
Mcm1 TTTCCTAATTAGGAAA TAGGAAA(1) TTTCCTAA(9) TTAGGAAA(10)   CCTAATTAGG(1) TTNCCNNNTNNGGAAA(1)
Met4 TCACGTG CACGTGA(1) TCACGTG(2)    CACGTGA(1) CACGTGAY(2)
  AAACTGTGG GTGGC(1) CCACA(3) TGTGG(5) CTGTG(6) CCACAGTT(3) AAACTGTGG(4)
   TGTGGC(2) CCACAGT(3) GCCACAC(4) ACTGTGG(5) AACTGTGG(7)  
Met31 AAACTGTGG TGTGGC(1) GCCACA(2) GCCACAC(2)   TGTGGCG(10) AAAANTGTGGC(4)
  TCACGTG CACGTGA(1) TCACGTG(3)    GCACGTGA(2) CACGTGANNT(7)
Stb1 ACGCGA AACGCG(4) TCGCGTT(3) TCGCGTT(3)   TTCGCGTT(3) AACGCSAAAA(3)
  CRCGAAA TTCGCG(1) TTTCGCG(1) TTTGGCG(2) TTTCGTG(5) CGCGAAAA(1) AACGCSAAAA(3)
  ACGCGT ACGCGT(3)     n/a n/a
Ste12 TGAAACA TGAAACA(1) ATGAAAC(2) TGAAACAA(2)   TGAAACA(2) ATGMAAC(13)
Swi4 CGCGAAA ACGCGAA(1) GACGCGA(2) AAACGCG(3) CACGAAA(7) GACGCGAA(1) RACGCGAAAA(2)
  ACGCGT AACGCGT(10)     n/a n/a
Swi5 CCAGCA GCTGG(1) CCAGC(2)    n/a n/a
Swi6 ACGCGT ACGCGT(1) AACGCGT(2) ACGCGTT(3)   AACGCGTT(2) AAACGCGW(4)
  ACGCGA AAACGCG(5) CGCGTTT(6) ACGCGAA(10) TTCGCGT(12) TTTCGCG(3) AAACGCGW(4)
  1. The table lists the motifs found by three algorithms which are closest to the known regulatory motifs of the 12 yeast cell-cycle TFs. Promoters were chosen based on the ChIP-chip experiments of Lee et al. [38]. The rankings from each algorithm are included in parentheses. The rankings for WordSpy are among the words of the same length.