Answer to Question #154937 in Bioinformatics for vaibhav

Question

(a) In order to calculate a multiple sequence alignment for N sequences, how many pair- wise alignments have to be calculated?

(b) Align the following using “star alignment” showing all intermediate steps:

S1= ATTCGGATT

S2= ATCCGGATT

S3= ATGGAATTTT

S4= ATGTTGTT

S5= AGTCAGG

Answer 1

a) 2 at a time.

b) To calculate the ‘center’ sequence, we compute all the pairwise alignment scores. Assume these pairwise alignment scores are givenin the following matrix

Summing pairwise scores in each row in the matrix, we obtain that $S_1$ is closest to all the other sequences. Hence, $S_1$ is selected to be at the center of the star.