Table 5.
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 |
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.