Ho = al_mat + penalty #The value for gap - horizontal.(from the left cell) P_mat = 0 #Return the first element of the pointer matrix back to 0.ĭi = al_mat + Diagonal(s1,s2,penalty) #The value for match/mismatch - diagonal. #Fill the matrix with the correct values. #Scans all the first columns element in the matrix and fill it with 'gap penalty' #Scans all the first rows element in the matrix and fill it with 'gap penalty' P_mat = np.zeros((m,n),dtype = str) #Initializes the alighment matrix with zeros. M = len(s2) + 1 #The dimension of the matrix rows.Īl_mat = np.zeros((m,n),dtype = int) #Initializes the alighment matrix with zeros. N = len(s1) + 1 #The dimension of the matrix columns. Penalty = #A dictionary for all the penalty valuse. #This function creates the aligment and pointers matricesĭef NW(s1,s2,match = 1,mismatch = -1, gap = -2):

Pointer = max(di,ho,ve) #based on python default maximum(return the first element). #This function gets the optional elements of the aligment matrix and returns the elements for the pointers matrix. #This function returns to values for cae of match or mismatch I have to fill 1 matrix withe all the values according to the penalty of match, mismatch, and gap.Īnd another matrix as pointers matrix - where 'v' for vertical, 'H' for horizontal and 'D' for diagonal.įor the sequences: TCGCA and TCCA, match:1, mismatch:-1 and gap:-2 I have to execute the needleman-wunsch algorithm on python for global sequence alignment.

Needleman wunsch algorithm python