Table 3

Discovered motifs using positive and negative data

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)

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.

Wang and Zhang Genome Biology 2006 7:R49   doi:10.1186/gb-2006-7-6-r49