BMC Bioinformatics

Table 3 Details for PWM and SiteGA models of TFBS recognition

From: Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

	General parameters		Specific parameters
TF type	No. of training sequences	Window length, nt	PWM Type of matrix¹	SiteGA Number of LPDs
E2F	40	38	DI	60
HNF4	29	17	DI	140
IRF1	28	33	DI	38
ISGF3	27	34	DI	36
NF-κB	43	30	DI	150
PPAR	37	25	DI	90
SF-1	53	30	DI	90
SREBP	37	18	MONO	110
STAT1	32	20	DI	150

¹ – DI – dinucleotide PWM, MONO – mononucleotide PWM.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com