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NMDetective
# Genome-wide predictions of NMD efficacy described in Lindeboom et al, Nature Genetics, 2019.
Non-overlapping bedGraphs of the NMDetectiveA and NMDetectiveB predictions are also accessible and visualized in the following UCSC genome browser sessions:
The NMDetective resource predicts the efficacy of nonsense-mediated mRNA decay for a pre-mature stop codon at every protein-coding nucleotide in the human and mouse genome. NMD scores range from ~0, indicating no mRNA degradation by NMD, to >0.52, indicating strong mRNA degradation. NMDetectiveA is a comprehensive prediction of NMD efficacy by Random Forest regression. NMDetectiveB is a simplified and fully transparent decision tree model that predicts NMD efficacy based on the EJC-model, distance to the start codon, and the length of the affected exon.
This fileset contains the NMDetectiveA and B predictions on the UCSC knownGene databases of the hg38, hg19, mm10 and mm9 genome builds in GTF/GFF2.2 format. The NMD scores are added as an attribute to each protein-coding exon as comma separated values per nucleotide.
Non-overlapping bedGraphs of the NMDetectiveA and NMDetectiveB predictions are also accessible and visualized in the following UCSC genome browser sessions: