PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
Fig 1
Example mRNA sequence showing the categorization of true positive and true negative start sites.
Suppose that a ribosome profiling experiment detected the following start sites for a given mRNA sequence: CUG at position -78 and CUG at position -120 (blue colored codons). These start sites were then assumed to be true positive start sites. In consequence, all near-cognate start sites not listed in the ribosome profiling dataset and upstream of the most downstream reported true start site were assumed to be true negatives (dark red colored codons). The light red colored codons are start sites not considered as false starts in the analyses since they are located downstream of the most downstream reported true start site. Note that the grey colored downstream part depicts the annotated CDS sequence whereas the italic (purple) upstream part marks the -99 upstream window needed to calculate some of the features (see below). All marked start sites (true positive and true negative) exhibit a surrounding window of ±99 nucleotides as well as a downstream in–frame stop codon. In total, this mRNA sequence would provide 2 true start sites and 9 false start sites out of 23 putative starts.