Sum Of Pairs Method

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

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updated 7.5 years ago by Biostar

• written 14.5 years ago by User 5037 •

1 answer

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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written 14.5 years ago by Michael Dondrup

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