Sum Of Pairs Method
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9.7 years ago
User 5037 ▴ 290

hi i just want to confirm my method of using sum of pairs is correct.

Lets say i have three sequences

ACCG_GTA
CGAAAA__
TT_GTGTA

Now to calculate the Multiple sequence aligment value using sum of pairs method i have to loop through the entire length of the MSA adding the sum of pairs in each column right ?

multiple scoring • 8.8k views
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Entering edit mode
9.7 years ago

Hi, I found these lecture slides. On page 3 it is explained how to calculate SP score with examples. So your statement seems to be correct given you want to sum up the pairwise alignment scores for each column.

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