Hello,
I'd like help understanding the logic of the dpal module in global mode.
It should find the best global alignment using the Needleman Wunsch algorithm correct?
However I see different behavior, for example when running the following (the m flag allows a gap of length 100, and g parameter for global mode):
./ntdpal -m 100 ACCCCTTTTTTTTTTTTT AT g
The output is:
|ACCCCTTTTTTTTTTTTT| |AT| G score=0.00 len=2 |16,0|17,1|
From the output I understand that the alignment created is:
ACCCCTTTTTTTTTTTTT
----------------AT
Meaning the alignment includes indels and at the end a T/A mismatch and a T/T match.
However the Needleman Wunsch algorithm in this case can give us the following alignment:
ACCCCTTTTTTTTTTTTT
A----------------T
In this case the created gap is of the same length but we have two matches - A/A and T/T.
So it seems this output has a better score.
Why are the outputs different in this case?
Or perhaps does the dpal module work a bit differently than the NW algorithm? If so, how?
Hello, I'd like help understanding the logic of the dpal module in global mode. It should find the best global alignment using the Needleman Wunsch algorithm correct? However I see different behavior, for example when running the following (the m flag allows a gap of length 100, and g parameter for global mode):
./ntdpal -m 100 ACCCCTTTTTTTTTTTTT AT gThe output is:
|ACCCCTTTTTTTTTTTTT| |AT| G score=0.00 len=2 |16,0|17,1|From the output I understand that the alignment created is:
Meaning the alignment includes indels and at the end a T/A mismatch and a T/T match. However the Needleman Wunsch algorithm in this case can give us the following alignment:
In this case the created gap is of the same length but we have two matches - A/A and T/T. So it seems this output has a better score.
Why are the outputs different in this case? Or perhaps does the dpal module work a bit differently than the NW algorithm? If so, how?
Thanks for the help.