Table 3 Open in new tab Selected... | Oxford Academic

Table 3

Open in new tab

Selected web-based resources for motif discovery tools

Algorithm	Motif model	Match model	Ref.
AlignACE	matrix	PWM	52
ANN-Spec	matrix	PWM	55
BioOptimizer	–	PWM	72
BioProspector	matrix, dyad	PWM	57
CAGER	–	–	73
Cis-analyst	–	PWM	74
CisModule	–	PWM	75
Cister	–	PWM	76
Clover	–	PWM	77
ClusterScan	–	PWM	78
CoBind	matrix, dyad	PWM	79
COMET	–	–	80
CompareProspector	–	–	57
ConsecID	–	PWM	81
Consensus	matrix	PWM	24
ConSite	–	PWM	82
COOP	–	reg.exp	83
cWinnower	string	mismatch	31
DMotifs	string	reg.exp	84
DMS	–	PWM	85
Dyad analysis	string, dyad	oligos	15
EC	string	fitness	39
EMnEM	–	–	68
FastM	–	PWM	18
FootPrinter	–	mismatch	71
FrameWorker	–	PWM	86
GANN	–	flexible	87
Gibbs sampler	matrix	PWM	44
Gibbs recursive	matrix	PWM	88
GLAM	string	–	89
GMS-MP	GWM	HMM	64
HMDM	–	DM	90
Improbizer	–	PWM	62
LOGOS	HMDM	DM	48
MAPPER	–	HMM	91
MCAST	–	PWM	92
MDScan	matrix	PWM	59
MEME	matrix	PWM	46
MERMAID	string	PWM	93
MISAE	–	mismatch	94
Mitra	string, dyad	mismatch	48
Mitra-dyad	–	mismatch	17
MITRA-PSSM	matrix	PWM	95
MM	–	PWM	96
MobyDick	string	mismatch	32
MoDEL	string	PWM	41
ModelGenerator	–	PWM	97
ModelInspector	–	PWM	97
Modulescanner	–	PWM	98
ModuleSearcher	–	PWM	98
MotifLocator	–	PWM	98
MotifPrototyper	–	DM	49
Motif regressor	–	PWM	41
Motif sampler	–	PWM	50
MSCAN	–	PWM	99
MultiProfiler	string	mismatch	21
NestedMICA	–	PWM	100
NONPAR	–	mixture	101
Oligo–analysis	string	oligos	102
OrthoMEME	–	PWM	69
Pattern–assembly	–	–	103
PhyloCon	–	PWM	66
PhyME	–	–	70
Pratt2	–	reg.exp	104
Projection	string	PWM	38
ProMapper	–	DM	105
PromoterInsp	–	oligos	106
QuickScore	string	IUPAC	107
REDUCE	–	PWM	108
SCORE	–	–	109
SeSiMCMC	–	PWM	63
SMILE	string, mult	mismatch	34
SOMBERO	–	PWM	110
Splash	–	reg.exp	111
Stubb	–	PWM	42
Teiresias	string	reg.exp	27
TFBScluster	–	PWM	112
Verbumculus	string	mismatch	35
Weeder	string	mismatch	36
Winnower	string	mismatch	30
YMF	string	reg.exp	113

Algorithm	Motif model	Match model	Ref.
AlignACE	matrix	PWM	52
ANN-Spec	matrix	PWM	55
BioOptimizer	–	PWM	72
BioProspector	matrix, dyad	PWM	57
CAGER	–	–	73
Cis-analyst	–	PWM	74
CisModule	–	PWM	75
Cister	–	PWM	76
Clover	–	PWM	77
ClusterScan	–	PWM	78
CoBind	matrix, dyad	PWM	79
COMET	–	–	80
CompareProspector	–	–	57
ConsecID	–	PWM	81
Consensus	matrix	PWM	24
ConSite	–	PWM	82
COOP	–	reg.exp	83
cWinnower	string	mismatch	31
DMotifs	string	reg.exp	84
DMS	–	PWM	85
Dyad analysis	string, dyad	oligos	15
EC	string	fitness	39
EMnEM	–	–	68
FastM	–	PWM	18
FootPrinter	–	mismatch	71
FrameWorker	–	PWM	86
GANN	–	flexible	87
Gibbs sampler	matrix	PWM	44
Gibbs recursive	matrix	PWM	88
GLAM	string	–	89
GMS-MP	GWM	HMM	64
HMDM	–	DM	90
Improbizer	–	PWM	62
LOGOS	HMDM	DM	48
MAPPER	–	HMM	91
MCAST	–	PWM	92
MDScan	matrix	PWM	59
MEME	matrix	PWM	46
MERMAID	string	PWM	93
MISAE	–	mismatch	94
Mitra	string, dyad	mismatch	48
Mitra-dyad	–	mismatch	17
MITRA-PSSM	matrix	PWM	95
MM	–	PWM	96
MobyDick	string	mismatch	32
MoDEL	string	PWM	41
ModelGenerator	–	PWM	97
ModelInspector	–	PWM	97
Modulescanner	–	PWM	98
ModuleSearcher	–	PWM	98
MotifLocator	–	PWM	98
MotifPrototyper	–	DM	49
Motif regressor	–	PWM	41
Motif sampler	–	PWM	50
MSCAN	–	PWM	99
MultiProfiler	string	mismatch	21
NestedMICA	–	PWM	100
NONPAR	–	mixture	101
Oligo–analysis	string	oligos	102
OrthoMEME	–	PWM	69
Pattern–assembly	–	–	103
PhyloCon	–	PWM	66
PhyME	–	–	70
Pratt2	–	reg.exp	104
Projection	string	PWM	38
ProMapper	–	DM	105
PromoterInsp	–	oligos	106
QuickScore	string	IUPAC	107
REDUCE	–	PWM	108
SCORE	–	–	109
SeSiMCMC	–	PWM	63
SMILE	string, mult	mismatch	34
SOMBERO	–	PWM	110
Splash	–	reg.exp	111
Stubb	–	PWM	42
Teiresias	string	reg.exp	27
TFBScluster	–	PWM	112
Verbumculus	string	mismatch	35
Weeder	string	mismatch	36
Winnower	string	mismatch	30
YMF	string	reg.exp	113

Table 3

Open in new tab

Selected web-based resources for motif discovery tools

Algorithm	Motif model	Match model	Ref.
AlignACE	matrix	PWM	52
ANN-Spec	matrix	PWM	55
BioOptimizer	–	PWM	72
BioProspector	matrix, dyad	PWM	57
CAGER	–	–	73
Cis-analyst	–	PWM	74
CisModule	–	PWM	75
Cister	–	PWM	76
Clover	–	PWM	77
ClusterScan	–	PWM	78
CoBind	matrix, dyad	PWM	79
COMET	–	–	80
CompareProspector	–	–	57
ConsecID	–	PWM	81
Consensus	matrix	PWM	24
ConSite	–	PWM	82
COOP	–	reg.exp	83
cWinnower	string	mismatch	31
DMotifs	string	reg.exp	84
DMS	–	PWM	85
Dyad analysis	string, dyad	oligos	15
EC	string	fitness	39
EMnEM	–	–	68
FastM	–	PWM	18
FootPrinter	–	mismatch	71
FrameWorker	–	PWM	86
GANN	–	flexible	87
Gibbs sampler	matrix	PWM	44
Gibbs recursive	matrix	PWM	88
GLAM	string	–	89
GMS-MP	GWM	HMM	64
HMDM	–	DM	90
Improbizer	–	PWM	62
LOGOS	HMDM	DM	48
MAPPER	–	HMM	91
MCAST	–	PWM	92
MDScan	matrix	PWM	59
MEME	matrix	PWM	46
MERMAID	string	PWM	93
MISAE	–	mismatch	94
Mitra	string, dyad	mismatch	48
Mitra-dyad	–	mismatch	17
MITRA-PSSM	matrix	PWM	95
MM	–	PWM	96
MobyDick	string	mismatch	32
MoDEL	string	PWM	41
ModelGenerator	–	PWM	97
ModelInspector	–	PWM	97
Modulescanner	–	PWM	98
ModuleSearcher	–	PWM	98
MotifLocator	–	PWM	98
MotifPrototyper	–	DM	49
Motif regressor	–	PWM	41
Motif sampler	–	PWM	50
MSCAN	–	PWM	99
MultiProfiler	string	mismatch	21
NestedMICA	–	PWM	100
NONPAR	–	mixture	101
Oligo–analysis	string	oligos	102
OrthoMEME	–	PWM	69
Pattern–assembly	–	–	103
PhyloCon	–	PWM	66
PhyME	–	–	70
Pratt2	–	reg.exp	104
Projection	string	PWM	38
ProMapper	–	DM	105
PromoterInsp	–	oligos	106
QuickScore	string	IUPAC	107
REDUCE	–	PWM	108
SCORE	–	–	109
SeSiMCMC	–	PWM	63
SMILE	string, mult	mismatch	34
SOMBERO	–	PWM	110
Splash	–	reg.exp	111
Stubb	–	PWM	42
Teiresias	string	reg.exp	27
TFBScluster	–	PWM	112
Verbumculus	string	mismatch	35
Weeder	string	mismatch	36
Winnower	string	mismatch	30
YMF	string	reg.exp	113

Algorithm	Motif model	Match model	Ref.
AlignACE	matrix	PWM	52
ANN-Spec	matrix	PWM	55
BioOptimizer	–	PWM	72
BioProspector	matrix, dyad	PWM	57
CAGER	–	–	73
Cis-analyst	–	PWM	74
CisModule	–	PWM	75
Cister	–	PWM	76
Clover	–	PWM	77
ClusterScan	–	PWM	78
CoBind	matrix, dyad	PWM	79
COMET	–	–	80
CompareProspector	–	–	57
ConsecID	–	PWM	81
Consensus	matrix	PWM	24
ConSite	–	PWM	82
COOP	–	reg.exp	83
cWinnower	string	mismatch	31
DMotifs	string	reg.exp	84
DMS	–	PWM	85
Dyad analysis	string, dyad	oligos	15
EC	string	fitness	39
EMnEM	–	–	68
FastM	–	PWM	18
FootPrinter	–	mismatch	71
FrameWorker	–	PWM	86
GANN	–	flexible	87
Gibbs sampler	matrix	PWM	44
Gibbs recursive	matrix	PWM	88
GLAM	string	–	89
GMS-MP	GWM	HMM	64
HMDM	–	DM	90
Improbizer	–	PWM	62
LOGOS	HMDM	DM	48
MAPPER	–	HMM	91
MCAST	–	PWM	92
MDScan	matrix	PWM	59
MEME	matrix	PWM	46
MERMAID	string	PWM	93
MISAE	–	mismatch	94
Mitra	string, dyad	mismatch	48
Mitra-dyad	–	mismatch	17
MITRA-PSSM	matrix	PWM	95
MM	–	PWM	96
MobyDick	string	mismatch	32
MoDEL	string	PWM	41
ModelGenerator	–	PWM	97
ModelInspector	–	PWM	97
Modulescanner	–	PWM	98
ModuleSearcher	–	PWM	98
MotifLocator	–	PWM	98
MotifPrototyper	–	DM	49
Motif regressor	–	PWM	41
Motif sampler	–	PWM	50
MSCAN	–	PWM	99
MultiProfiler	string	mismatch	21
NestedMICA	–	PWM	100
NONPAR	–	mixture	101
Oligo–analysis	string	oligos	102
OrthoMEME	–	PWM	69
Pattern–assembly	–	–	103
PhyloCon	–	PWM	66
PhyME	–	–	70
Pratt2	–	reg.exp	104
Projection	string	PWM	38
ProMapper	–	DM	105
PromoterInsp	–	oligos	106
QuickScore	string	IUPAC	107
REDUCE	–	PWM	108
SCORE	–	–	109
SeSiMCMC	–	PWM	63
SMILE	string, mult	mismatch	34
SOMBERO	–	PWM	110
Splash	–	reg.exp	111
Stubb	–	PWM	42
Teiresias	string	reg.exp	27
TFBScluster	–	PWM	112
Verbumculus	string	mismatch	35
Weeder	string	mismatch	36
Winnower	string	mismatch	30
YMF	string	reg.exp	113