An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA

Dutta, Shayoni; Madan, Spandan; Parikh, Harsh; Sundar, Durai

doi:10.1186/s12864-016-3323-9

Table 3 Comparison of ZifNN predictions with other tools reported in literature. ZiFNN, ZiFiT [6] and Zinc Finger Tools [4] were compared with experimental data mined from literature (K_D and helix prediction)* using Hamming distance as the metric

From: An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA

DNA Target 5′ → 3′	References from Literature	Experimentally Found ZFP			Best prediction made by ZiFNN	Identity for ZiFNN	ZiFit Prediction			Identity for ZiFiT	Zinc Finger Tools			Identity for Zinc Finger Tools
DNA Target 5′ → 3′	References from Literature	F1	F2	F3	Best prediction made by ZiFNN	Identity for ZiFNN	F1	F2	F3	Identity for ZiFiT	F1	F2	F3	Identity for Zinc Finger Tools
GTGGAGGAA	[57]	QSGNLTRRSGHLTRRSGELTR			DSGHLTRDSGHLTRDSGHLTR	0.76	RNVNLVTRQDNLGRQASNLLR			0.33	RSDELVRRSDNLVRQSSNLVR			0.47
GCTGCTGCT	[58]	RSGELTRTSGELTRRSGELTR			TSGELTETSGELTETSGELTE	0.76	LRASLRRQRSDLTRMKNTLTR			0.38	TSGELVRTSGELVRTSGELVR			0.76
GAGGAGGAT	[59]	QSGNLTRRSGNLTRRSGNLTR			QSGHLTRQSGHLTRQSGHLTR	0.76	-			-	RSDNLVRRSDNLVRTSGNLVR			0.66
CTGGCGGCA	[60]	RSGALTERSGDLTRQSGDLTR			RSGDLTTRSGDLTTRSGDLTT	0.76	-			-	RNDALTERSDDLVRQSGDLRR			0.76
GGGGCGGGG	[61]	KSGHLTARSGELTRRSGHLTK			RSGHLTRRSGHLTRRSGHLTR	0.80	RKHRLDGRTDTLARRGNHLRR			0.33	RSDKLVRRSDDLVRRSDKLVR			0.42
GCTGGGGGC	[62]	RSGELTRTSGHLTRDSGHLTR			QSGHLTRQSGHLTRQSGHLTR	0.80	VSNSLARRREHLVRTNSKLTR			0.42	TSGELVRRSDKLVRDPGHLVR			0.61
GCGTGGGGA	[63]	RSGELTRRSGHLTRQSGHLTR			QSGTLTRRSGTLTRQSGTLTR	0.80	-			-	RSDDLVRRSDHLTTQRAHLER			0.61
GCGTGGGCA	[64]	RSGELTRRSGHLTRRSGELTR			RSGTLTRRSGTLTRRSGTLTT	0.80	-			-	RSDDLVRRSDDLVRQSGDLRR			0.57
GCGTGGGAA	[63]	RSGELTRRSGHLTRQSGNLTR			RSGTLTRRSGTLTRRSGTLTR	0.80	-			-	RSDDLVRRSDHLTTQSSNLVR			0.66
GCGGGCCGC	[65]	RSGELTRDSGALTRRSGELTR			RSGHLTRRSGHLTRRSGHLTR	0.80	-			-	RSDDLVRDPGHLVRHTGHLLE			0.47
GCAGCGGAC	[62]	RSGELTRRSGHLTRQSGSLTR			QSGHLTRQSGHLTRQSGHLTR	0.80	QKGTLGRRTDTLARDPSNLIR			0.38	QSGDLRRRSDDLVRDPGNLVR			0.52
GAGGAAGGG	[59]	RSGHLTRQSGNLTRRSGNLTR			QSGHLTRQSGHLTRQSGHLTR	0.80	RRDNLNRQQTNLTRKRERLDR			0.48	RSDNLVRQSSNLVRRSDKLVR			0.61
ACTACTGGA	[60]	TSGDLTRTSGDLTRQSGHLTR			TSGELTRTSGELTRTSGELTR	0.80	-			-	THLDLIRTHLDLIRQRAHLER			0.57
GCTGGGGGC	[62]	QSGDLTRRSGHLTRDSGHLTR			QSGHLTRQSGHLTRQSGHLTR	0.85	VSNSLARRREHLVRTNSKLTR			0.48	TSGELVRRSDKLVRDPGHLVR			0.61
GAAGAGGGT	[59]	QSGHLTRRSGNLTRQSGNLTR			QSGHLTRQSGHLTRQSGHLTR	0.85	QRNNLGRRQDNLGRTRQKLET			0.38	QSSNLVRRSDNLVRTSGHLVR			0.61
GAGGAAGGT	[66]	TSGHLTRTSGHLTRRSGELTR			TSGHLTRTSGHLTRTSGHLTR	0.90	RRDNLNRQQTNLTRTKQRLEV			0.28	RSDNLVRQSSNLVRTSGHLVR			0.47
					Average for ZifNN	0.81	Average For ZiFit			0.38	Average for Zinc Finger Tool			0.58

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us