实验四-基于Matlab的序列比对分析3-25(常用版).doc

实验四_基于Matlab的序列比对分析3-25（常用版）
(可以直接使用，可编辑 完整版资料，欢迎下载）
实验四 基于Matlab的序列比对分析
实验目的
1． 了解MATLAB7.x生物信息工具箱中的序列比对方法；
2． 熟悉从数据库获取序列信息, 查找序列的开放阅读框, 将核普酸序列转换为氨基酸序列, 绘制比较两氨基酸序列的散点图, 用Needleman-wunsch算法和Smith-Waterman算法进行比对, 以及计算两序列的同一性的方法；
3． 熟悉与序列比对相关的生物信息学函数。
所需软件
MATLAB 7.0或MATLAB 7.0以上的版本

实验内容
序列比对是生物信息学的重要基础。进行序列比对的目的之一是判断两个序列之间是否具有足够的相似性，从而判定二者之间是否具有同源性。序列比对的基本算法主要有两个，一个是用于全局比对的Needleman-Wunsch算法，另一个是主要用于局部比对的Smith-Waterman算法，而后者又是在前者的基础上发展起来的。在MATLAB生物信息工具箱中，序列比对主要用这两种算法。
确定两个序列的相似性是生物信息学的基础工作，通过序列比对（又称序列联配），可以确定两个序列是否具有同源性。

1. 查找序列信息
Tay-Sachs症是一种由于缺乏ß-氨基已糖苷酶A（Hex A）而导致的常染色体隐性遗传疾病。这种酶能分解大脑和神经细胞中的神经节苷脂（GM2）。基因HEXA编码该酶的ß亚基，而第三个基因GM2A编码活化剂蛋白质GM2。
1.1 查找目的基因Tay-Sachs
在NCBI（）上查找信息，在Search列表中选择[Nucleotide],在for框中输入[Tay-Sachs], 点击Go。

1.2 读入序列数据
查找结果返回编码酶HexA的α和β亚基的基因和编码活化剂酶的相关页面。NCBI中人类基因HEXA的登录号是NM_000520。用fastaread或genbankread函数可将基因信息被以结构列表的形式导入MATLAB工作区。
方式1：
HumanHEXA = fastaread('NM_000520.fasta');
humanHEXA=getfield(HumanHEXA,'Sequence')；
方式2：
HumanHEXA = genbankread('NM_000520.gb')；
humanHEXA=getfield(HumanHEXA,'Sequence')
1.3 读入另一序列的信息mouseHEXA
许多基因的序列和功能通过同源基因在进化过程中被保留下来。同源基因就是有共同祖先或是相似序列的基因。查找公共数据库的目的之一就是找出相似的基因。如果用户能在数据库中定位一个未知的基因，那么这个未知基因和已知基因的功能和特征很可能是相同的。
用fastaread或genbankread函数可将鼠类HEXA基因信息被以结构列表的形式导入MATLAB工作区（NCBI中鼠类基因HEXA的序列号是AK080777）。
方式1：
MouseHEXA = fastaread('AK080777.fasta');
mouseHEXA=getfield(MouseHEXA, 'Sequence')
方式2：
MouseHEXA = genbankread('AK080777.gb')；
mouseHEXA=getfield(MouseHEXA, 'Sequence')
2． 确定蛋白质编码序列
一个核苷酸序列在蛋白质编码段的前后都包含了调控序列。通过分析这个序列，可以确定在编码最终蛋白质中亚氨基酸的核苷酸。
2.1 查找人类HEXA的ORF
使用seqshoworfs函数输出人类HEXA的所有阅读框中ORF中起始和终止密码子的位置。
humanORFs = seqshoworfs(humanHEXA)
结果显示了三个阅读框的ORF, 分别以蓝色、红色和绿色标记, 其中最长的ORF在第1个阅读框。
阅读框部分省略
阅读框部分省略

阅读框部分省略

2.2确定鼠类HEXA的ORF
使用seqshoworfs函数输出人类HEXA的所有阅读框中ORF中起始和终止密码子的位置。
mouseORFs = seqshoworfs(mouseHEXA)
结果得到三个阅读框的ORF, 分别以蓝色、红色和绿色标记, 其中最长的ORF在第一个阅读框。

Frame 1

阅读框部分省略
阅读框部分省略

阅读框部分省略
3. 比较氨基酸序列
在确定核苷酸序列中的ORF之后，就可以将核苷酸序列的蛋白质编码段转换为相应的氨基酸序列。并使用比对功能来确定两序列的相似性。
3.1 将ORF转换为氨基酸序列
mouseProtein = nt2aa(mouseHEXA);
由于人类的ORF在第一个阅读框, 所以需要指出其位置
humanProtein = nt2aa(humanHEXA,'Frame',1);
3.2 绘制散点图
比较人类和鼠类的氨基酸序列。
seqdotplot(humanProtein,mouseProtein,4,1)
ylabel('Human hexosaminidase A');
xlabel('Mouse hexosaminidase A');

散点图是确定两序列相似性最简单的方法之一。图中对角线平直连续, 表示这两个序列相似性较好。
3.3 比对这两个氨基酸序列
下面nwalign函数有目的地比对两序列。采用的是Needleman-wunsch算法, 可返回全局比对的计算统计量。
[globalscore, globalAlignment] = nwalign(humanProtein,mouseProtein)
showalignment(globalAlignment);

Identities = 486/753 (65%), Positives = 570/753 (76%)
3.4 截短序列
寻找终点：
humanStops = find(humanProtein == '*')
mouseStops = find(mouseProtein == '*')
下面将序列截短至只含第一个甲硫氨酸至第一个停止符,进行局部比对。截短序列至只包含蛋白质的氨基酸序列和停止符。

humanSeq = humanProtein(70:humanStops(2));
humanSeqFormatted = seqdisp(humanSeq)
mouseSeq = mouseProtein(11:mouseStops(1));
mouseSeqFormatted = seqdisp(mouseSeq)
3.5 比对被截短的氨基酸序列
[globalscore, globalalignment] = nwalign(humanSeq,mouseSeq);
showalignment(globalalignment);
Identities = 450/540 (83%), Positives = 507/540 (94%)

3.6 局部比对两氨基酸序列
下面swalign函数有目的地比对两序列。采用的是Smith-Waterman算法, 可返回局部比对的计算统计量。
[localscore, localAlignment] = swalign(humanProtein,mouseProtein);
showalignment(localAlignment);
Identities = 454/547 (83%), Positives = 514/547 (94%)

作业
1．进入NCBI任意搜索两条细菌条斑病基因组序列（不同物种，搜索词为bacterial streak），按照序列比对的步骤进行序列比对，进行如下操作并列出结果：
查找序列的开放阅读框, 将核普酸序列转换为氨基酸序列, 绘制比较两氨基酸序列的散点图, 用Needleman-wunsch算法和Smith-Waterman算法进行比对, 以及计算两序列的同一性。

Unit 13
Section One Tactics for Listening
Part 1 Spot dictation
Sister Rivers Build Cultural Bridge Between U.S. and China
The Mississippi is the major river system in the United States, flows almost 3,800 kilometers from a small lake in Minnesota, gathering the waters of 250 other rivers and streams before reaching the Gulf of Mexico.
In mid-May, as spring flowers began to open, about 41 students from a dozen colleges, mostly in the Midwest, explored a section of the river in Wisconsin and Iowa, to learn about the environment, and each other.
The students, from the U.S., China and around the world, came to join the River Spirit Exchange program.
The cross-cultural educational experience set up by the University of Wisconsin, Madison-based Environment and Public Health Network for Chinese Students - focuses on the Mississippi and China's longest river, the Yangtze.
This three-day get-together featured story-telling, hiking, camping and canoeing, all part of a larger lesson about conservation projects that can be used on both the Yangtze and Mississippi.
After the group met at the Crane Foundation preserve, they headed south to canoe a stretch of the Kickapoo River that winds its way through southwestern Wisconsin before joining the Mississippi. They paddled along a stretch of the Kickapoo River, where a 20-year preservation venture stopped encroachment by developers and protected the natural setting of the waterway.
The students on the River Spirit Exchange ended their first night with singing and stories around the campfire. Organizers say the success and spirit of this first gathering of students will lead to other trips, including one down the Yangtze.
Part2 Listening for Gist
Four out of five of all children who got leukemia* in 1960 died. Now four out of every five survive. The secret of this miraculous change is the rosy periwinkle*, a forest flower which tribal doctors had used for centuries. The United States National Cancer Institute has identified more than 2,000 tropical rainforest plants with ability to fight cancer. In fact, about 4,000 of all drugs given out in the United States today owe much of their strength to chemicals from wildlife, largely from the rainforest.
Other drugs include quinine, which comes from a South American tree, and sufferers from high blood pressure get relief from the snakeroot* plant from Indian forests. The armadillo*, of South America is helping us find a cure for leprosy*.

Directions: Listen to the passage and write down the gist and the key words that help you decide.
1. This passage is about some wildlife from forests that can be used in the treatment of certain diseases.
2. The key words are leukemia, survive, change, forest flower, 2,000 tropical rainforest plants, fight cancer, quinine, a South American tree, high blood pressure, snakeroot, armadillo, leprosy.

Section Two Listening Comprehension
Part1 dialogue
How to Succeed

Dario: I think the most important thing you must have to succeed in Italy is er ... of course, you have to be ambitious, because if you are not ambitious you can't reach your aim, your target. And you must have also a natural ability*, because you must adapt yourself and your work and er ... enjoy your work, of course. And Italian people are used to working a lot and to doing hard work. Of course you must also know the right people because if you want a job and you don't know anybody you have to work much harder.
Interviewer: So if you were going to choose one factor, Dario, which one do you think would be the most important? Could you choose one?
Dario: Yes, ambition.
interviewer: Thank you.
(Dialogue B)
Sue: I think that to be successful in Spain you need ambition, because it's what makes you want to work and do something different. And I think natural ability is also important. To be a good musician and to succeed I think that you must have something special. And I think that knowing the right people is important because it can save you a lot of time. You don't spend so much time trying to get something if you know people that can help you.
Interviewer: What would you say is the most important thing?
Sue: Ambition I think is the most important.

(Dialogue C)
Taylor: I think the most important things are hard work, and good education, and natural ability.
The Japanese have a traditional culture and we think that working industriously is a virtue, so laziness cannot be accepted by society. And a good education - anyone who wants to and who makes the effort can enter the famous universities, so er ... when we estimate someone's ability we look at whether he's graduated from university or not. But if someone wants to succeed, of course he needs ambition and natural ability.
Interviewer: So for you, which is the most important factor?
Taylor: Oh, in Japan, hard work, definitely
Exercise
Directions: You are going to listen to three people talking about how they succeeded in different countries. Take notes and complete the following grid.

Country
Profession
Quality required
The most important factor
A
Italy

Ambitious, adaptive, communicative
Ambition
B
Spain
Musician
Ambitious, having natural ability, being able to know the right people
Ambition
C
Japan

Hard working, well-educated, ambitious, having natural ability
Hard work

Part 2 passage
Global Economy of the 21st Century
1. The move toward a global economy has been further strengthened by the widespread adoption of liberal economic policies.
2. Current trends suggest that the world is moving rapidly toward an economic system that is more favorable for the practice of international business.
3. The world may be moving toward a more global economic system, but globalization is not inevitable.
4. It is simply worth noting that even from a purely economic perspective, globalization is not all good.
5. The opportunities for doing business in a global economy may be significantly enhanced, but the risks associated with global financial contagion are greater.

The last quarter of the century has seen rapid changes in the global economy. Barriers to the free flow of goods, services, and capital have been coming down. The volume of cross-border trade and investment has been growing more rapidly than global output, indicating that national economies are becoming more closely integrated into a single, interdependent, global economic system. As their economies advance, more nations and areas are joining the ranks of the developed world. A generation ago, South Korea and Singapore were viewed as second-tier developing areas. Now they boast powerful economies, and their firms are major players in many global industries from shipbuilding and steel to electronics and chemicals. The move toward a global economy has been further strengthened by the widespread adoption of liberal economic policies by countries that for two generations or more were firmly opposed to them. Thus, following the normative prescriptions of liberal economic ideology, in country after country we are seeing state-owned businesses privatized, widespread deregulation*, markets being opened to more competition, and increased commitment to removing barriers to cross-border trade and investment. This suggests that over the next few decades, countries such as the Czech Republic, Poland, Brazil, China, and South Africa may build powerful market-oriented economies. In short, current trends suggest that the world is moving rapidly toward an economic system that is more favorable for the practice of international business.
On the other hand, it is always hazardous to take established trends and use them to predict the future. The world may be moving toward a more global economic system, but globalization is not inevitable. Countries may pull back from the recent commitment to liberal economic ideology if their experiences do not match their expectations. Clearly, this would be a tougher world for international businesses to compete in.
Moreover, greater globalization brings with it risks of its own. This was starkly demonstrated in 1997 and 1998 when a financial crisis in Thailand spread first to other East Asian nations and then in 1998 to Russia and Brazil. Ultimately the crisis threatened to plunge the economies of the developed world, including the United States, into a recession. It is simply worth noting that even from a purely economic perspective*, globalization is not all good. The opportunities for doing business in a global economy may be significantly enhanced, but as we saw in 1997-1998, the risks associated with global financial contagion* are also greater. Still, there are ways for firms to exploit the opportunities associated with globalization, while at the same time reducing the risks through appropriate hedging* strategies.
A: Pre-listening Question
What will affect the future of global economic development besides political factors?
The following two factors must be taken into consideration although there are many others that will decide the future of the development. One is that the food and energy situation will become worse and worse with the increasing world population. The other is that our living environment has now been heavily polluted as a result of the booming of modem industries.

B: Sentence Dictation
Directions: Listen to some sentences and write them down. You will hear each sentence three times.

C: Detailed Listening
Directions: Listen to the passage and complete the following sentences.
1. The rapid changes have taken place in the past 25 years in the global economy because barriers to the free flow of goods, services, and capital have been coming down.
2. The volume of cross-border trade and investment results in establishing a single, interdependent, and global economic system.
3. The examples of economic development in South Korea and Singapore show that more nations are joining the ranks of the developed world.
4. The move towards a global economy has been further strengthened by the widespread adoption of liberal economic policies.
5. The current trends indicate that the world is moving rapidly to an economic system that is more favorable for the practice of international business.
6. This world would be a tougher world for international businesses to compete in if some countries pull back from the recent commitment to liberal economic ideology because their experiences do not match their expectations.
7. What we can learn from the East Asia financial crisis in 1998 is that globalization brings risks of its own.
8. The writer still believes that there are ways for companies to exploit the opportunities associated with globalization in the 21st century

D: After-listening Discussion
Directions: Listen to the passage again and discuss the following questions.
1. Greater globalization brings with it risks of its own. This was starkly demonstrated in 1997 and 1998 when a financial crisis in Thailand spread first to other East Asian nations and then in 1998 to Russia and Brazil. Ultimately the crisis threatened to plunge the economies of the developed world, including the United States, into a recession. It is simply worth noting that even from a purely economic perspective, globalization is not all good. The opportunities for doing business in a global economy may be significantly enhanced, but the risks associate