[1] Databases of multiple sequence alignments Text-based searches of CDD, Pfam (profile HMMs), PROSITE Database searches with a query sequence with BLAST, CDD, PFAM [2] Multiple sequence alignment by manual input PileUp, CLUSTAL W, CLUSTAL X
Conclusions: assessment of alternative multiple sequence alignment algorithms
[2] “Orphan” sequences are highly divergent members of a family. Surprisingly, orphans do not disrupt alignments. Also surprisingly, global alignment algorithms outperform local.
Conclusions: assessment of alternative multiple sequence alignment algorithms
[4] When proteins have large N-terminal or C-terminal extensions, local alignment algorithms are superior. PileUp (global) is an exception.
Paralogs (共生同源)
Homologous sequences within a single species that arose by gene duplication. 以上两个概念代表了两个不同的进化事件用于分子 进化分析中的序列必须是直向同源的，才能真实反映进 化过程。
common carp
How to calculate similarity?
1. To install BioEdit, DNAstar, etc 2. Some tools online
同源性的两种类型
Orthologs (直向同源)
Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function.
Pairwise sequence alignment programs
Multiple sequence alignment programs
How to get multiple sequences? Sequence BLAST Program
Two kinds of multiple sequence alignment resources
2 分子进化分析介绍
2.1 分子进化研究的目的 从物种的一些分子特性出发，从而了 解物种之间的生物系统发生的关系。
蛋白和核酸序列 通过序列同源性的比较进而了解基因的进 化以及生物系统发生的内在规律。
2.2 系统发育树是什么？
对一组实际对象的世系关系的描述（如基因， 物种等）。 已发展成为多学科（包括生命科学中的进 化论、遗传学、分类学、分子生物学、生物化 学、生物物理学和生态学，又包括数学中的概 率统计、图论、计算机科学和群论）交叉形成 的一个边缘领域。闻名国际生物学界的美国冷 泉港定量生物学会议于1987年特辟出"进化树"专 栏进行学术讨论，标志着该领域已成为现代生 物学的前沿之一，迄今仍很活跃。
一个系统发育树
末端分支 末端 物种 顶端 叶子 中间节点 中间枝条 节点
根
树只代表分支的拓扑结构
A
BC
D
F E†
G
D
C E†
F
G A
B
2.3 分子进化研究的基础 假设
核苷酸和氨基酸序列中含有生物进化历史的 全部信息。
2.3 分子进化研究的基础 理论
在各种不同的发育谱系及足够大的进化 时间尺度中，许多序列的进化速率几乎 是恒定不变的。（分子钟理论， Zuckerkandl and Pauling 1965 ）
Multiple sequence alignment algorithms
Local Progressive
Global
CLUSTAL PileUp other
PIMA
Iterative
DIALIGN
SAGA
PIMA
Strategy for aቤተ መጻሕፍቲ ባይዱsessment of alternative multiple sequence alignment algorithms
2.3 分子进化研究的基础 实际
虽然很多时候仍然存在争议，但是分子 进化确实能阐述一些生物系统发生的内 在规律。
分子钟理论
从一个分歧数据可以推测其他
y 序列分歧度
x
分歧时间
趋同进化的基因
(genes have converged function by separate evolutionary paths)
[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.
RBP: 26 RVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVA 59 + K++ + ++ GTW++MA + L + A QTKQDLELPKLAGTWHSMAMA-TNNISLMATLKA 55
glycodelin: 23
Similarity
The extent to which two (nucleotide or amino acid) sequences are similar.
BaliBase: comparison of multiple sequence alignment algorithms
Conclusions: assessment of alternative 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
Paralogs: members of a gene (protein) family within a species
Odorant-binding protein 2A
Lipocalin 1
10 changes
speciation
paralogs orthologs
Erik L.L. Sonnhammer Orthology,paralogy and proposed classification for paralog subtypes TRENDS in Genetics Vol.18 No.12 December 2002 http://tig.trends.co m 0168-9525/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.
Multiple sequence alignment programs AMAS Genedoc ClustalW ClustalX DIALIGN HMMT Match-Box MultAlin MSA Musca PileUp SAGA T-COFFEE
1. ClustalW in BioEdit
Conclusions: assessment of alternative multiple sequence alignment algorithms
[3] Separate multiple sequence alignments can be combined (e.g. RBPs and lactoglobulins). Iterative algorithms (PRRP, SAGA) outperform progressive alignments (ClustalX)
zebrafish
rainbow trout teleost
Orthologs: members of a gene (protein) family in various organisms. This tree shows RBP orthologs.
African clawed frog chicken human mouse rat horse pig cow rabbit 10 changes