A hybrid method for the exact planted (l, d) motif finding problem and its parallelization

BMC Bioinformatics

Table 5 Application of the PHEP_PMSprune(ons) on the real yeast dataset

Transcription Factor	Genes	Detected motif (s) & parameters	Published Motif (s) & reference(s)	Time
PHO4 (600 bp)	PHO5, PHO8, PHO81, PHO84,	CACGTG (6,0)	CACGT[G\|T] [38]	38 (5%)
HSE_HSTF (600 bp)	SSA1, HSP26, SSA4, HSC82, SIS1, CUP1-1	TTCAGTGAA (9,2)	TTCNNGAA [38] TTCNNNGAA [38]	37 (35%)
PDR (600 bp)	PDR3, SNQ2, PDR15, HXT9, HXT11, PDR5, YOR1	TCCGTGGA (8,1) TCCGCGGA (8,1)	TCCG[C\|T]GGA [38]	27(13%)
MCB (600 bp)	CDC2, CDC9, CDC6, CLN1, POL1, CDC21	ACGCGT (6,0)	[A\|T]CGCG[A\|T] [38]	31(20%)
ECB (600 bp)	SWI4, MCM5 MCM7, CDC6 CLN3	TTTCCCATTAAGGAAA (16,3)	TTtCCcnntnaGGAAA [10, 39]	41(49%)

The first column includes the transcriptional factors (regulatory elements) and the length of upstream sequences. The second column includes the regulated genes. The first three factors and their related genes are available at the SCPD [38]. The ECB is the early-cell-cycle-box promoter region described in [39] and we extracted its related genes from the Yeast Genome Database [37]. The third column includes the motif detected by our tool and the respective parameters (l, d). The fourth column includes the published motifs and their references. The final column includes the running time in seconds needed to run our program in the parameter range from (6, 0) until (21, 3), i.e., there are 64 invocation of our program. The percentages in brackets refer to percentage improvements in rum time compared to PMSprune method.

ISSN: 1471-2105