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View Code? Open in Web Editor NEWAffine gap sequence alignment in Python.
Affine gap sequence alignment in Python.
Hi Sir
Can you provide a sample fasta file containing sequences to see how does it work?
The code in alignment.py
does not seem capable of identifying the best alignment.
Take sequences GAAAAAAA
and GTTTTTTT
for example. It will generate the alignment:
G A A A A A A A _ _ _ _
G _ _ _ _ T T T T T T T
With the score:
1 + -10 + -0.5 + -0.5 + -0.5 + -0.5 + -4 + -4 + -4 + -10 + -0.5 + -0.5 + -0.5 + -0.5 = -35
But the following alignment:
G A A A A A A A _ _ _ _ _ _ _
G _ _ _ _ _ _ _ T T T T T T T
Has a better score:
1 + -10 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 + -10 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 + -0.5 = -26
It seems like the implementation of the algorithm from Gotoh, O. An improved algorithm for matching biological sequences. J Mol Biol 162, 705โ708 (1982)
is incorrect
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