def nwprofile(S, gap, seq, residues,sc):
'''A function that performs the global alignment of a sequence to a profile'''
f=frequency(S,residues)
M=PSSM(seq,sc,residues,S)
F=[[0.0] * (len(f)+1) for i in range (0, len(seq)+1)]
for i in range(1, len(seq)+1):
for j in range(1, len(f)+1):
F[i][j]=max([F[i-1][j]+gap, F[i][j-1]+gap, F[i-1][j-1]+M[i-1][j-1]])
return F[i][j]
return F
def smprofile(S, gap, seq, residues,sc):
'''A function that performs the local alignment of a sequence to a profile'''
f=frequency(S,residues)
M=PSSM(seq,sc,residues,S)
F=[[0.0] * (len(f)+1) for i in range (0, len(seq)+1)]
for i in range(1, len(seq)+1):
for j in range(1, len(f)+1):
F[i][j]=max([F[i-1][j]+gap, F[i][j-1]+gap, F[i-1][j-1]+M[i-1][j-1],0.0])
maxscore=0
for i in range(1, len(seq)+1):
for j in range(1, len(f)+1):
if F[i][j]>maxscore:
maxscore=F[i][j]
print F
print maxscore
