Patent Document ID: 7774185
Application ID: 10940192
Patent Flag: 1

Claim One:
1. A method for detecting alignments for protein sequences, the method comprising: generating respective data sets for two protein sequences, wherein such a data set represents protein blocks having n successive C-alpha atoms of a primary amino acid sequence; determining, for the data sets, respective first and second matrices of distances of protein atoms from said C-alpha atoms, wherein the distance matrices have respective distance matrix elements, the distance matrix elements having respective numerical values; determining a difference matrix from said first and second distance matrices, wherein the difference matrix has numerical difference matrix elements; and determining alignments for the protein sequences based upon the difference matrix, wherein determining the alignments includes the steps of: forming, by a processor of a suitably programmed computer system, a model having a set of logical cells in a memory of the computer system, the cells having respective binary logical states, wherein the cells of the model form a matrix such that for each of the difference matrix elements there is a corresponding one of the cells of the model; and performing iterations in which the states of the cells in the memory are selectively altered, including ones of the cells being altered responsive to binary logic states of respectively neighboring ones of the cells.