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BCB 567/CprE 548
Fall 2007
Homework 5
Due Tuesday, Dec 4
Note:
Use constant gap penalty and the following parameters, unless otherwise speciﬁed
α
denotes the score of a match,
β
denotes mismatch penalty, and
γ
denotes the gap penalty.
1. (4 points) Let
s
1
,s
2
,...,s
k
be
k
sequences, each of length
n
. What is the maximum
possible SPscore of a multiple sequence alignment between them? What is the worst
possible SPscore?
2. (4 points) Devise an example of three (short) sequences
s
1
,
s
2
and
s
3
such that the induced
alignment of
s
1
and
s
2
has a lower score than the optimal pairwise alignment of
s
1
and
s
2
.
3. (5 points) Consider generalizing the
k
band algorithm for the multiple sequence alignment
of
r
sequences, of length
n
each. Derive a stopping condition for the same.
4. (5 points) In the center star method, the multiple alignment is constructed by successively
aligning each new string to the center string
s
c
. The
order
in which the strings are aligned
to
s
c
is not speciﬁed. Argue that the same multiple alignment is built, regardless of the
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 Fall '06
 OLIVEREULENSTEIN

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