How to generate it?
How do we generate a multiple alignment? There is an obvious solution:
Given a
pairwise alignment, just add the third, then the fourth, and so on
, until all have
been aligned. But is this as straightforward as it looks? Consider a case with three
short fake sequence that are pairwise homologous in the following way:
dront
...AGAC.
..
trex
...AC.
..
dront
...AGAC.
..
unicorn .
..AG.
..
trex
...AC.
..
unicorn .
..AG.
..
It is not selfevident how these sequences are to be aligned together. Here are some
possibilities:
dront
...AGAC.
..
trex
...AC.
..
unicorn .
..AG.
..
dront
...AGAC.
..
trex
...AC.
..
unicorn .
..AG.
..
dront
...AGAC.
..
trex
...AC.
..
unicorn .
..AG.
..
A multiple alignment depends in a nontrivial way on the various parameters
(insertion/deletion penalties, substitution coefficients,.
..), and, importantly, also
on the
order
in which sequences are added to the growing multiple alignment.
In pairwise alignments, one has a twodimensional matrix with the sequences on each
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 Fall '10
 LauraChoudry
 Chemistry, Vector Space, Computational complexity theory, pairwise alignment

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