iTriplet, a rule-based nucleic acid sequence motif finder

Table 3 iTriplet prediction using real biological sequences.

Gene:	Preproinsulin (IEB1) promoter+5' UTR		Remarks
iTriplet	GTYYGGAAAYTGCAGCYTCAGCCCC		<25,2> model
PMSprune	CAGCCTCAGCCCC TT		Ref. [17]
MITRA	CCTCAGCCCCC		Ref. [14]
Published	CTCAGCCCCCAGCCATCTGCCGACCCCCCC		Transfac ID: R04457
Gene:	DHFR (promoter+5' UTR)		Remarks
iTriplet	RWSTSGCGCSAAAC Y		<15,3> model
PMSprune	ATTTCG TG GGCA		Ref. [17]
MITRA	TGCAATTTC GCGCCA AAC		Ref. [14]
Published	ATTTCGCGCCAAA		Transfac ID: R01928
Gene:	Metallothionein promoter+5' UTR		Remarks
iTriplet	TTTTGCRC TCG YCCC		<15,1> model
PMSprune	CTCTGC AC ACGG CCC		Ref. [17]
MITRA	TGCGCCCGG		Ref. [14]
Published	TGCGCCCGG		Transfac ID: R08298
Gene:	c-fos serum response element promoter+5' UTR		Remarks
iTriplet	CCATATTAGGAC ATCTGCGT		<20,1> model
PMSprune	CCA AATTT G		Ref. [17]
MITRA	CCATATTAGGACA		Ref. [14]
Published	CAGGATGTCCATATTAGGACATC		Transfac ID: R00466
3'UTR Regulatory Elements	iTriplet Prediction only	Published	Remarks
AU-rich (ARE)	TTTTATTTATTTT T	WWTTATTTATTWW	<14,3> model
Cytoplasmic Polyadenylation element (CPE)	TTTTAAT	TTTTAT and TTTTAAT	<6,1> model
Pumillio binding element (PBE)	T KT WAATA	TGTAAATA	<8,1> model

Motif predicted by iTriplet is presented in consensus sequence. Bold and underlined sequence represents correctly predicted nucleotide. Transfac IDs are obtained from TRANSFAC database [37]

ISSN: 1748-7188