http://tcoffee.crg.cat/apps/tcoffee/do:regular
多序列比对软件——MAFFT
rpm –ivh mafft-7.305-gcc_fc6.x86_64.rpm 必须有root权限
Download and installation
多序列比对软件——MAFFT
Align X (1) 序列的输入
(2) 序列alignment
(3) 结果的编辑（ Metafile; text ）
Multalin
http://multalin.toulouse.inra.fr/multalin/
T-Coffee
Multiple Sequence Alignment Tools
Definitions: two types of homology 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.
运行步骤
(1) (2) (3) 序列的输入，1，输入序列的名称 序列alignment 选择，2，1，或者其他选项 运行，
(4)
结果导出
进到下面这个文件夹 cd src/ 运行即可 ./clustalw2
Clustal W
Bioedit
/clustalv
Software
1. ClustalX +Treeview 2. Mega 3.1
/mega.html
进化树的应用
1. 新基因的鉴定 2. 新蛋白的分类
蛋白质功能预测
1. 同源蛋白功能推测； 2. 蛋白质结构域或基元分析。
Pattern and profile searches
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
Sequence alignment of S_TKc domain of PXK_v1 with consensus S_TKc domain. Identical residues are represented in black and similar residues in gray. The subdomains of the S_TKc domain are indicated with Roman numerals. Asterisks denote the indispensable residues of lysine, glutamine and aspartic acid in consensus S_TKc domain.
Sequence alignment of Homo sapiens Sgt1.2 with its five homologous proteins. Numbers on the right refer to the last amino acid in each corresponding line. Residues indicated with dark shading are identical amino acids. Grey shading represents 80-90% similarity and light grey means 60-70% similarity.
生物信息学
第五章 多序列比对和进化树分析
Part I
Sequence alignment
Definitions
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.
Genedoc
(1) 序列的输入 (2) 序列alignment
(3) 格式调节
(4) 输出到绘图内编辑
Alignment of A. ferrooxidans SOD protein and its orthologs. Atf27230: A. ferrooxidans ATCC 27230, De195: Dehalococcoides ethenogenes 195 Gspca: Geobacter sulfurreducens PCA, Tad1728: Thermoplasma acidophilum DSM 1728. Identical residues have been boxed and are shaded in dark.
African clawed frog chicken human horse pig cow 10 changes rabbit
mouse rat
apolipoprotein D retinol-binding protein 4 Complement component 8 Alpha-1 Microglobulin /bikunin
Multiple sequence alignment programs How to get multiple sequences?
Sequence format BLAST Program
Multiple sequence alignment programs
Genedoc
Clustal X Clustal W Align X MultAlin T-Coffee MAFFT
Paralogs Homologous sequences within a single species that arose by gene duplication.
common carp
zebrafish
rainbow trout teleost
Orthologs: members of a gene (protein) family in various organisms. This tree shows RBP(视黄醇结合蛋白) orthologs.
2.采用ClustalW在线分析（ AAQ84722.1 ）
Paralogs: members of a gene (protein) family within a species
prostaglandin D2 synthase progestagenassociated endometrial protein neutrophil gelatinaseassociated lipocalin
Clustal X
(1) 序列的输入 (2) 序列alignment
Clustal W
ClustalW（命令行）是ClustalX（图形版）的姊妹版，在DOS或linux下运行 安装：
首先解压压缩包 tar -xzvf clustalw-2.1.tar.gz 进到解压后的文件夹 cd clustalw-2.1 安装 ./configure make
Definitions
Homology Similarity attributed to descent from a common ancestor.
Identity The extent to which two (nucleotide or amino acid) sequences are invariant. Similarity The extent to which two (nucleotide or amino acid) sequences are similar.
Odorant-binding protein 2A
Lipocalin 1
10 changes
How to calculate similarity and identity?
1. Align X 2. MatGAT 3. Bioedit
Align X
Align X is one of the standalone of Vector NTI suite Not easy to get the cracked version
SMART
http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1
InterProScan
Motifscan
作业
1.采用Genedoc软件分析（ AAQ84722.1 ）
要求：4个ortholog蛋白质序列alignment，每 排 80个氨基酸残基，采用二色（黑色标记一 致氨基酸残基），每一个比较的蛋白质给出 Genbank登录号
多序列比对文件美化
GeneDoc Boxshade Espript TEXshade WebLogo/SeqLogo JProfileGrid
多序列比对结果特征提取
Protein alignment based DNA alignment
http://www.cbs.dtu.dk/services/RevTrans/