多序列比对和进化树分析(含gen).ppt

利用现代分子生物学技术所获得的生物多样性的信息 ,可大致分为以下两大类:1）离散特征数据 (discrete character data)，即所获得的是 2个或更多的离散的值 ,是赋给某一具体的运筹分类单位（operational taxonomic unit ,简称OTU）的；2）相似性和距离数据 (similarity and distance data)，它并不是某一具体分类单元所具有,而是用彼此间的相似性或距离所表示出来的各分类单位间的相互关系。 离散特征法则主要包括MP法（最大简约法）和ML法（最大似然法）。 距离法在构成距离矩阵（故而也称距离矩阵法）后，要么通过某个标准来筛选出进化树的最佳估计，可以用最小二乘标准来估计进化树，称最小二乘进化树；或者根据某种算法得到一个聚类的树形图，不必对每个树都进行比较，计算量小，因此也不一定是最佳的树，常见的有UPGMA法（类平均法）和NJ法（neighbor-joining method，邻接法）。 1. ClustalX +Treeview 2. Mega 3 Software /mega.html * * 序列间比对 Pairwise alignment The process of lining up two or more sequences to achieve maximal levels of identity (and conservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology. Definitions Homology Similarity attributed to descent from a common ancestor. Definitions Identity The extent to which two (nucleotide or amino acid) sequences are invariant. RBP: 26 RVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVA 59 + K++ + ++ GTW++MA + L + A glycodelin: 23 QTKQDLELPKLAGTWHSMAMA-TNNISLMATLKA 55 Definitions Similarity The extent to which two (nucleotide or amino acid) sequences are similar. How to calculate similarity? 1. To install Vector NTI Suite 7.0 2. To use Align X program. Orthologs Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. Paralogs Homologous sequences within a single species that arose by gene duplication. Definitions: two types of homology Orthologs: members of a gene (protein) family in various organisms. This tree shows RBP orthologs. common carp zebrafish rainbow trout teleost African clawed frog chicken mouse rat rabbit cow pig horse human 10 changes Paralogs: members of a gene (protein) family within a species apolipoprotein D retinol-binding protein 4 Complement component 8 prostaglandin D2 synthase neutrophil gelatinase- associated lipocalin 10 changes Lip