new06多序列比对和进化树分析.pptxVIP

第一节 多序列比对;多序列比对的定义 ;; 我们称比对前序列中残基的位置为绝对位置。如序列Ⅰ的第3位的残基是甘氨酸G，则绝对位置Ⅰ3就是甘氨酸，而不能变成任何其它氨基酸。相应地，我们称比对后序列中残基的位置为相对位置。显然，同一列中所有残基的相对位置相同，而每个残基的绝对位置不同，因为它们来自不同的序列。 绝对位置是序列本身固有的属性，或者说是比对前的位置，而相对位置则是经过比对后的位置，也就比对过程赋予它的属性。 ;Pairwise alignment The process of lining up two 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.;;Multiple sequence alignment programs;Two kinds of multiple sequence alignment resources;AMAS Genedoc ClustalW ClustalX DIALIGN HMMT Match-Box MultAlin MSA Musca PileUp SAGA T-COFFEE;ClustalW in BioEdit 序列的输入 序列alignment 格式调节 输出到绘图内编辑;1. ClustalW in BioEdit;;;;;;2. Clustal W online 序列的输入 序列alignment; ;Multiple sequence alignment algorithms;PIMA;[1] Create or obtain a database of protein sequences for which the 3D structure is known. Thus we can define “true” homologs using structural criteria. [2] Try making multiple sequence alignments with many different sets of proteins (very related, very distant, few gaps, many gaps, insertions, outliers). [3] Compare the answers.;BaliBase: comparison of multiple sequence alignment algorithms;[1] As percent identity among proteins drops, performance (accuracy) declines also. This is especially severe for proteins 25% identity. Proteins 25% identity: 65% of residues align well Proteins 40% identity: 80% of residues align well;[2] “Orphan” sequences are highly divergent members of a family. Surprisingly, orphans do not disrupt alignments. Also surprisingly, global alignment algorithms outperform local.;[3] Separate multiple sequence alignments can be combined (e.g. RBPs and lactoglobulins). Iterative algorithms (PRRP, SAGA) outperform progressive alignments (ClustalX);[4] When proteins have large N-terminal or C-terminal extensions, local alignment algorithms are superior. PileUp (global) is an exception.; 多序列比对的软件