Question: How Do I Calculate The Overall Gap Penalty
0
gravatar for User 5037
8.4 years ago by
User 5037290
User 5037290 wrote:

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 ?

sequence • 6.6k views
ADD COMMENTlink modified 8.4 years ago by Niklas60 • written 8.4 years ago by User 5037290
7

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

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k
1

Your example appears to be improperly aligned.

ADD REPLYlink written 8.4 years ago by Neilfws48k
1

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.

ADD REPLYlink written 8.3 years ago by DG7.1k

here the final two A's are matches.

ADD REPLYlink written 8.4 years ago by User 5037290

homework example?

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k

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

ADD REPLYlink written 8.4 years ago by User 5037290

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

ADD REPLYlink written 8.4 years ago by User 5037290

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

ADD REPLYlink written 8.4 years ago by Fabian Bull1.3k

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.

ADD REPLYlink written 8.4 years ago by User 5037290
0
gravatar for Niklas
8.4 years ago by
Niklas60
Niklas60 wrote:

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 ;-)

ADD COMMENTlink modified 8 months ago by RamRS27k • written 8.4 years ago by Niklas60

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.

ADD REPLYlink written 8.4 years ago by User 5037290
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