Question

The input for the neural network includes parameters for sequence physical properties, such as ______

(a) DNA bendability

(b) Signals such as the TATA box

(c) Signals such as initiator box

(d) Signals such as CpAA islands

This question was addressed to me in semester exam.

This interesting question is from Prediction Algorithms in division Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Right choice is (d) Signals such as CpAA islands

The best I can explain: As seen, the correct answer is CpG in option d. The hidden layer combines all the features to derive an overall likelihood for a site being a promoter. Another unique feature is that McPromoter does not require that certain patterns must be present, but instead the combination of all features is important. For instance, even if the TATA box score is very low, a promoter prediction can still be made if the other features score highly. The program is currently trained for Drosophila and human sequences.