Features and labels

[Mohamed-ElhajAbdou]

Hello, i have two questions hope i get the answers from you

1- first the rule of the sequence alignment is that to extract a chunks of subsequences represents the first sequence

2- and then those alignments are fed to the covariance matrix to extract a matrix called covariance matrix the measures the correlations between each of these alignments with each other

3-from what i understand it that proteins contact map describe the distance matrix as a label , like for example the distance between the first amino acid in the first chain and the first amino acid in the second chain is equal to 200 A, we set a threshold with 8 A so the proteins contact map description for this distance number will be "not in contact" "False" or in binary world "0" is im right with that understanding

My Questions
First
1-what is the rule of the covariance matrix
2- what is the rule of proteins contact map are those the labels of the matrix distances if so what is the rule of the covariance matrix
3- what is the input to the neural network model
A- what is the feature, are those the distance matrix if yes what is the rule of covariance matrix
B- what is the label of these features are Proteins contact map is the labels in (0's and 1's )

Second
1- i want from you kindly to give me a hint or steps which is the first script to use and second and so on cuz i want to cite your paper so i started to inspired from your great work

thanks in advance