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Table 5 5'-UTR Sequence Properties Utilized for Analyses by the Artificial Neural Network (ANN)

From: Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites

Parameters Description Range
Consensus Sequence Patterns
Pattern #1 (C/(G/C) Position -6/-7 Yes/No
Pattern #2 (Kozak) Position -3/+4 Yes/No
Consensus Sequence Patterns
5'-UTR Length Length of 5'-UTR 80 to 2000 bp
ORF Length Length of ORF from the annotated start codon to the stop codon 350 to 5000 bp
Start Codon Frequency of aTIS in training set 0 to1
Number of AUGs Number of upstream AUGs from aTIS 0 to 19
G/C Ratio Normalized ratio of G to C -1 to 1
Secondary Structure
Free Energy 50 bp UnaFold -40 to 0
Secondary Structure UnaFold 0 = stem, 3 = loop
  1. Properties of 5'-UTR sequences of mRNAs using aTIS are shown according to their application in the ANN. The derivation of each feature is shown, as well as the range of representation to the ANN for training and testing. These features are implemented in the ANN analyses which includes refined representations of secondary structure.