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Assignment 4 (Ch 6 & 7) Name: SOO NAM Started: March 9, 2009 11:11pm Attempt: 2 / 3 Finished: March 9, 2009 11:27pm Out of: 19 Time spent: 15 min. 55 sec.
Question 1
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Consider a brass alloy the stress-strain behavior of which is show

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Materials 1M03, Test #1 2014
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Feb. 4, 2014
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MATERIALS 1M03
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Question 1 True or false?
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It is possible to produce a

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Question 1
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Consider a brass alloy the stress-strain behavior of which is shown

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Question 1
_ point defects occur when impurity atoms fill

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Name: AHMED OSMAN Started: January 19, 2009 8:33pm Question 1 (1 point) True or False:
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Crystals are never perfect at the

Assignment 4 (Ch 6 & 7)
ZIQI WANG Started: March 19, 2010 9:50 PM Questions: 14
1.
(Points: 1) When the load is released on a specimen that has been experienced only elastic deformation, all of the strain is recovered immediately.
a. True b. False
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1
156
CHAPTER 9. GENE PREDICTION
application of these techniques to eukaryotes is complicated by the exon-intron
structure. The average length of exons in vertebrates is 130 bp, and thus exons are
often too short to produce peaks in the sliding window plo

CHAPTER 10. GENOME REARRANGEMENTS
202
breakpoint
graph
+6
-2
| +5
-1
+3
-7_j
+9
B
-4
reversal on cycle C
interleaving
graph
-2
-8
+6
+7
-3
-9
+1
-5
^
J fci
A V
? D
B
m
<
Figure 10.13: Reversal on a cycle C complements the edges between the neighbors of C

163
9.4. SPLICED ALIGNMENT
Figure 9.6: Assembling.
Then (9.1) can be rewritten as
(S(i-lJ-l,k)
ifzV first(k)
Scfw_iJ,k) =max
P(firstcfw_k)J
- 1) + S(gi,tj), if i = first(k)
if i first(k)
(9.2)
where
P(i,j) = max <
(9.3)
. jost(fc)=i-i -

10.8. SEARCHING FOR SAFE REVERSALS
203
implies (i) ( C , D) is not an edge in Hn and (ii) (D, E) is an edge in Hw. Therefore,
by lemma 10.12, reversal a preserves the edge cfw_D,E) in Hna. If both vertices
D and E belong to V(C)9 then lemma 10.12 implies

180
CHAPTER 10. GENOME REARRANGEMENTS
eliminating breakpoints. An observation that every reversal can eliminate at most
2 breakpoints immediately implies that d(n) > 4 ^ , where b(n) is the number of
breakpoints in TT. Based on the notion of a breakpoint,

128
CHAPTER 7. MULTIPLE ALIGNMENT
Proof We use an averaging argument.
minG6c; Ccfw_G) S(AG) < ^ G e a C(G) S(AG)
5(i4) = ^ 0 S(A)
Here the inequality holds for an arbitrary alignment A, and in particular, it holds
for an optimal alignment.
Lemmas 7.2 and

130
CHAPTER 7. MULTIPLE ALIGNMENT
is not trivial. Pevzner, 1992 [265] solved the case of I = 3 by mapping the problem
to maximum matching in graphs. Bafna et al, 1997 [18] further designed a 2 - |
approximation algorithm for arbitrary I.
7.6 Dot-Matrices

166
CHAPTER 9. GENE PREDICTION
Figure 9.9: Selecting the best exon assembly.
After the optimal block assembly is found, the hope is that it represents the correct exon-intron structure. This is almost guaranteed if a protein sufficiently similar
to the on

170
CHAPTER 9. GENE PREDICTION
marker available today for diagnosing and monitoring patients with prostate cancer.
The questions of what other important alternatively spliced variants of these and
other genes are implicated in cancer remains open. Moreove

10.4. EXPECTED REVERSAL DISTANCE
0
2
4
6
8/
10 \
189
12
10
IV
3 /5
7
9
11
12
14
13
Figure 10.8: G(ju) and G(ji3).
Proof For n < 2, the claim is trivial. For n > 2, partition the vertex set of G(jn)
into Vi = cfw_0,1,3 and VJ. From lemma 10.1 and the fact

134
CHAPTER 8. FINDING SIGNALS IN DNA
A common-sense approach to the magic word problem is to test all words of
length I and to find those that appear in all (or almost all) sequences from the
sample (Staden, 1989 [326], Wolfertstetter et al., 1996 [370],

148
CHAPTER 8. FINDING SIGNALS IN DNA
Figure 8.3: Profile HMM.
8.10 Profile HMM Alignment
Given a family of functionally related biological sequences, one can search for
new members of the family using pairwise alignments between family members
and sequen