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Table 4 MCC distributions (Average MCC, Maximum MCC and Minimum MCC) of tmRNA and RNaseP secondary structure predictions done with the P-DCfold algorithm using all sequences and using different homologous sequence selection models (M HC , M G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=rr8vbqabaaaaa@3A84@ , M G C MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbwvMCKfMBHbqedmvETj2BSbqee0evGueE0jxyaibaieYdOi=BI8qipeYdI8qiW7rqqrFfpeea0xe9LqFf0xc9q8qqaqFn0dXdHiVcFbIOFHK8Feei0lXdar=Jb9qqFfeaYRXxe9vr0=vr0=LqpWqaaeaabiGaaiaacaqabeaabeqacmaaaOqaamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaGabaiab=ntinnaaBaaaleaacqWFge=rcqWFce=qaeqaaaaa@3BB7@ and M G C + G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=jq8djabgUcaRiab=zq8hjab=rr8vbqabaaaaa@3EE4@ ). The percentage of predictions with MCC > 75 are also given.

From: Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

 

tmRNA

RNAseP

 

All

M HC

M G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=rr8vbqabaaaaa@3A84@

M G C MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbwvMCKfMBHbqedmvETj2BSbqee0evGueE0jxyaibaieYdOi=BI8qipeYdI8qiW7rqqrFfpeea0xe9LqFf0xc9q8qqaqFn0dXdHiVcFbIOFHK8Feei0lXdar=Jb9qqFfeaYRXxe9vr0=vr0=LqpWqaaeaabiGaaiaacaqabeaabeqacmaaaOqaamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaGabaiab=ntinnaaBaaaleaacqWFge=rcqWFce=qaeqaaaaa@3BB7@

M G C + G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=jq8djabgUcaRiab=zq8hjab=rr8vbqabaaaaa@3EE4@

All

M HC

M G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=rr8vbqabaaaaa@3A84@

M G C MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbwvMCKfMBHbqedmvETj2BSbqee0evGueE0jxyaibaieYdOi=BI8qipeYdI8qiW7rqqrFfpeea0xe9LqFf0xc9q8qqaqFn0dXdHiVcFbIOFHK8Feei0lXdar=Jb9qqFfeaYRXxe9vr0=vr0=LqpWqaaeaabiGaaiaacaqabeaabeqacmaaaOqaamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaGabaiab=ntinnaaBaaaleaacqWFge=rcqWFce=qaeqaaaaa@3BB7@

M G C + G U MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83mH00aaSbaaSqaaiab=zq8hjab=jq8djabgUcaRiab=zq8hjab=rr8vbqabaaaaa@3EE4@

Avg MCC

45.19

56.82

63.38

67.66

67.45

41.03

60.27

73.58

70.13

75.3

Max MCC

89

85

84

80

85

86

84

85

80

85

Min MCC

10

26

41

56

41

5

30

56

56

56

% MCC > 75

1.3%

8.6%

5.7%

27.6%

26.7%

0.7%

18%

48.6%

23.3%

60.4%