4 Multiple Sequence Alignment 4.1 Multiple sequence alignment

Grundlagen der Bioinformatik, SS’09, D. Huson, May 10, 2009 43endchoose two sub-alignments C ∗ p, C ∗ q from C;C := C − {C ∗ p, C ∗ q }C ∗ s := align(C ∗ p, C ∗ q );C := C ∪ {C ∗ s }until |C| = 1return the alignment contained in C4.9.1 Pair-guided alignmentA very simple method for merging two sub-alignments (in this context usually called profiles) is pairguidedalignment. Two specific sequences are chosen, one from each profile. These two are alignedand the final alignment is produced following this pairwise alignment.Let the two profiles beALEE A-EREA-EE ALER--LEEAlign e.g. the first sequence of first profile with the last of second:ALEE-ALER-The resulting multiple alignment is then:ALEE-A-EE--LEE-A-EREALER-4.9.2 Profile alignmentIn practice, a more sophisticated approach is used.Suppose we are given two profiles A 1 ∗ = {A 1 , . . . , A r } and A 2 ∗ = {A r+1 , . . . , A n }. Here, we discussthe alignment of profiles in the case of the SP-score and linear gap scores. In this case, we can sets(−, a) = s(a, −) = −d and s(−, −) = 0 for all a ∈ A 1 ∗ or A 2 ∗ .Definition 4.9.2 (Profile alignment) A profile alignment of A 1 ∗ and A 2 ∗ is an MSA⎧⎪⎨A ∗ =⎪⎩A ∗ 1 = a ∗ 11 , a∗ 12 , . . . , a∗ 1L. . .A ∗ r = a ∗ r1 , a∗ r2 , . . . , a∗ rLA ∗ r+1 = a ∗ r+1,1 , a∗ r+1,2 , . . . , a∗ r+1,L. . .A ∗ n = a ∗ n1 , a∗ n2 , . . . , a∗ nL ,obtained by inserting whole columns of gaps into either A 1 ∗ or A 2 ∗ , without changing the alignmentof either of the two profiles.