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BioInformatics Quiz1 Week4

The document is about Markov models and their application to sequence alignment. It contains 7 multiple choice questions testing understanding of first-order Markov models, calculating transition probabilities, and using hidden Markov models to predict coding and noncoding regions in a DNA sequence.

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4K views7 pages

BioInformatics Quiz1 Week4

The document is about Markov models and their application to sequence alignment. It contains 7 multiple choice questions testing understanding of first-order Markov models, calculating transition probabilities, and using hidden Markov models to predict coding and noncoding regions in a DNA sequence.

Uploaded by

chahoub
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Bioinformatics: Introduction and Methods 生物信息学: 导论与方法

Week 4
Markov Model

Markov Model
Submit your assignment
Due DateNov 16, 7:59 AM CET
Attempts3 every 8 hours
Receive grade
To Pass80% or higher
Grade
—
Markov Model
Graded Quiz • 30 min

Due Nov 16, 7:59 AM CET

Markov Model

Total points 7
1.
Question 1

In first-order Markov Models, the probability distribution of the current state depends
and only depends on ______.

在一阶马尔科夫链中，当前状态的概率分布与且只与______有关.

1 point

all previous states

前面所有状态

its own state

自己的状态

the immediate previous state

前一个状态
the immediate next state

后一个状态

2.
Question 2

Use the Markov Model to perform two sequences alignment, giving the following
state transition graph (M means two residues align together, X means there is a
insertion in the first sequence, Y means there is a insertion in the second sequence)

利用马尔可夫模型进行双序列比对，给定如下状态转移图（M 表示两个残基匹
配，X 表示第一条序列存在一个插入，Y 表示第二条序列存在一个插入）

If the gap open probability is 0.1 and gap extension probalibity is 0.7

已知 gap open 的概率为 0.1，gap extension 的概率为 0.7

What's the transition probability of the blue edge in the above graph?

则上面状态转移图中蓝色边上的状态转移概率值为______

1 point

0.1

0.2
0.3

0.8

3.
Question 3

In question 2, what's the transition probability of the green edge in the graph?

在第 2 题的状态转移图中，绿色边上的状态转移概率值为______

1 point

0.2

0.3

0.7

0.8

4.
Question 4

Given the following state transition graph and emission probabilities for each state

给定如下状态转移关系和每个状态下的生成概率
What's the probability of observing "aabbc" through state transition path 1-2-2-3-3?

则通过状态转移路径 1-2-2-3-3 观测到序列 aabbc 的概率是多少？

1 point

0.00072

0.004068

0.000144

0.00336

5.
Question 5

In the following simple Hidden Markov Model of coding and noncoding region
prediction, the left matrix is the log10 result of transition probability matrix and the
right matrix is the log10 result of emission probability matrix(In the state transition
probability matrix, the value in row i column j is the log10 probability from state i
transfer to state j)

对于下面这个简单的预测编码区非编码区的隐马尔可夫模型，其中两个矩阵分
别为状态转移概率矩阵和生成概率矩阵取 log10 后的结果（在状态转移概率矩
阵中，第 i 行第 j 列表示从状态 i 转移到状态 j 的概率取 log10 后的结果）

For the above model, using dynamic programming, predict coding region(c) and
noncoding region(n) of sequence "CGAAAA" (the log10 initial probability of
noncoding is -0.1 and log10 initial probability of coding is -0.7 )

应用上述模型，采用动态规划的方法，对序列 CGAAAA 进行编码区(c)和非编


码区(n)预测 （初始状态为非编码区的概率取 log10 后设为-0.1，初始状态为编
码区的概率取 log10 后设为-0.7）：
Q: What's the value in the green block?

Q: 则绿色格子的值为多少？

1 point

-2.0

-1.5

-1.3

-2.1

6.
Question 6

In question 5, what's the value in the blue block?

在第 5 题中，蓝色格子的值为多少？

1 point

-2.0

-1.5
-2.1

-0.7

7.
Question 7

In question 5, the end of this sequence (A) is identified as coding or noncoding?

在第 5 题中，序列的尾部（A）被鉴定成编码还是非编码？

1 point

coding

noncoding

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