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Table 2 Accuracy of REANNOTATE's inferences relative to manual annotation

From: Automated paleontology of repetitive DNA with REANNOTATE

 

Defragmentation

Nesting

Time

 

Sensitivity

Specificity

  

maize (AF123535.1)

97.8%

100.0%

100.0%

100.0%

wheat (AF459639.1)

96.0%

100.0%

93.3%

90.9%

  1. Accuracy of predictions in the Defragmentation layer of re-annotation is given by their sensitivity and specificity according to the formulas T P T P + F N MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqWGubavcqWGqbauaeaacqWGubavcqWGqbaucqGHRaWkcqWGgbGrcqWGobGtaaaaaa@3443@ and T N T N + F P MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqWGubavcqWGobGtaeaacqWGubavcqWGobGtcqGHRaWkcqWGgbGrcqWGqbauaaaaaa@343F@ respectively, where TP is the count of true positives, TN true negatives, FP false positives, and FN the count of false negatives (see Implementation) relative to the manual annotations. Here a 'prediction' refers to a sequence similarity hit reported by REPEAT MASKER that has been defragmented into a TE model by REANNOTATE. For the Nesting Structure and Time layers accuracy is given as the proportion of predictions in agreement with the original manual annotation [45, 51].
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BMC Genomics

ISSN: 1471-2164

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