Sum Of Pairs Method

Question

[User 5037]

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 ?

Answer 1

[Michael]

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.