实验四-基于Matlab的序列比对分析3-25(常用版).doc
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1、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
2、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-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HEX
3、A编码该酶的亚基,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的和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(HumanH
4、EXA,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
5、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
6、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
7、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
8、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(hu
9、manProtein = *)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, globalalignm
10、ent = 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 = 454/5
11、47 (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 C
12、ultural Bridge Between U.S. and ChinaThe 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, abou
13、t 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 ex
14、perience - set up by the University of Wisconsin, Madison-based Environment and Public Health Network for Chinese Students - focuses on the Mississippi and Chinas longest river, the Yangtze. This three-day get-together featured story-telling, hiking, camping and canoeing, all part of a larger lesson
15、 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 s
16、tretch 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 spiri
17、t of this first gathering of students will lead to other trips, including one down the Yangtze.Part2 Listening for GistFour 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 wh
18、ich 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,
19、 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 passa
20、ge 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 Sout
21、h American tree, high blood pressure, snakeroot, armadillo, leprosy. Section Two Listening ComprehensionPart1 dialogueHow 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 cant reach
22、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 do
23、nt 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 ambit
24、ion, because its 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
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