Question

Which of the following is untrue regarding PHD?

(a) It stands for Profile network from Heidelberg

(b) It is a web-based program that combines neural network only

(c) It first performs a BLASTP of the query sequence against a non redundant protein sequence database

(d) In initial steps it finds a set of homologous sequences, which are aligned with the MAXHOM program (a weighted dynamic programming algorithm performing global alignment)

The question was posed to me in class test.

My enquiry is from Protein Secondary Structure Prediction  for Globular Proteins in portion Secondary Structure Prediction of Bioinformatics

Answer 1

Correct answer is (b) It is a web-based program that combines neural network only

The best explanation: It is a web-based program that combines neural network with multiple sequence alignment. After the initial steps, the resulting alignment in the form of a profile is fed into a neural network that contains three hidden layers. The first hidden layer makes raw prediction based on the multiple sequence alignment by sliding a window of thirteen positions.