Hi, I need to calculate PSSM profiles of a number of proteins. I've used biopython but it gives me a matrix of sequence length *20 for a whole multiple sequence alignment ... , actually what I need is a matrix with rows representing each protein sequence in the alignment , with fixed length , so that I can use in machine learning.
I also tried the R package "protr" but it gives me a variable length matrix ..!!
Some references say that it can be calculated using PSI-BLAST
I spent too much time trying to figure out how to calculate it but I couldn't find any reference...
Please, could any one help me to solve this problem ?