Smith Waterman for 3 Sequences

[julx5]

Hi all,

I haven written a code for the alignment of 3 sequences by building
up a 3D-Scorematrix ( taking into account 7 neighbours).
However, we are also asked to say whether it is possible to find an optimal
local alignment by using the classic Smith-Waterman for 2 Sequences
multiple times pairwise to get an alignment for 3 sequences.

In my opinion there is no optimal local alignment by using the classic alg.
pairwise, since you do not take int oaccount the actual 3D-space concurrently while building the 3d-matrix.
Are there any more detailed explanations on that? And if the pairwise approach works fine what would be the computational complexity in o-notation?

Thanks

julx5