How Do I Calculate The Overall Gap Penalty

Question

[User 5037]

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 ?

[Michael Schubert]

by the way, a gap is never aligned to a gap in a two-sequence alignment

[Neilfws]

Your example appears to be improperly aligned.

[DG]

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.

[User 5037]

here the final two A's are matches.

[Michael Schubert]

homework example?

[User 5037]

ok. Now i edited my question. Yeah its not properly aligned but is it possible to find the alignment score for it ?

[User 5037]

@MichaelSchubert Cant you calculate the alignment score when there are gaps on the same column on both sequences ?

[Fabian Bull]

I know division by zero is not proper but is it possible?

[User 5037]

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.

Answer 1

[Niklas]

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 ;-)

[User 5037]

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.