Hi all. Iam trying to calculate the alignment score of these two sequences
A_TAAG_A
A_G____A
match = 1 mismatch = -1 gap opening = -5 gap continuation = -1
no of matches = 2 no of mismatches = 1
how do i calculate gap penalty ? Could someone please help me out
Cant you calculate the alignment score when there are gaps on the same column on both sequences ?
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User 5037 •
Hello there,
since I do not completey understand your example, (why are the A's matches, but not in the same column?) i will simply point you to a set of slides, which I find explain the matter well:
http://www.bioinf.uni-freiburg.de/Lehre/Courses/2010_SS/V_Bioinformatik_1/gap-penalty-gotoh.pdf
They are part of this lecture of Freiburg University in Germany (slides are all in english though)
I hope this helps you in helping yourself ;-)
Yeah the A on the fist and last column match. I found it difficult to align it with the web browser editor. But somehow now i managed to do it.
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here the final two A's are matches.
homework example?
by the way, a gap is never aligned to a gap in a two-sequence alignment
Your example appears to be improperly aligned.
ok. Now i edited my question. Yeah its not properly aligned but is it possible to find the alignment score for it ?
@MichaelSchubert Cant you calculate the alignment score when there are gaps on the same column on both sequences ?
I know division by zero is not proper but is it possible?
hey i had this confusion after i played the game pylo. Pylo seemed to calculate the overall alignment score even if there were gaps on the same column.
Technically gaps in the same column could be constituted as a match, but they are also a gap opening penalty. In real alignment scoring you would never place a gap character in the same column in both sequences of a pairwise sequence alignment, you just wouldn't. They are completely meaningless in this context. If I had to calculate the score here I would ignore them.