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March 19, 2019 23:58
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Nussinov algorithm for bioinformatics from pseudo code provided in class
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grid = [ | |
[0,None,None,None], | |
[0,0,None,None], | |
[-1,0,0,None], | |
[-1,-1,0,0], | |
] | |
seq = ['U','G','A','U'] | |
def match(i,j): | |
return 'A' in (seq[i],seq[j]) and 'U' in (seq[i],seq[j]) | |
return 'C' in (seq[i],seq[j]) and 'G' in (seq[i],seq[j]) | |
return 0 | |
while grid[0][len(grid) - 1] is None: | |
for row_index, row in enumerate(grid): | |
for col_index, col in enumerate(row): | |
if col is None: | |
bot_right = grid[row_index+1][col_index] | |
left = grid[row_index][col_index-1] | |
bot_left = grid[row_index+1][col_index-1] + match(row_index,col_index) | |
other_one = max( | |
[grid[row_index][k] + grid[k+1][row_index] | |
for k in range(row_index,col_index)] | |
) | |
grid[row_index][col_index] = max(bot_right,left,bot_left) | |
break | |
for row in grid: | |
print(row) |
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