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Alignment - PowerPoint PPT Presentation


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Alignment. 陳致嘉. Questions. Question 1: 假設現在有 1 條未知的蛋白質 , 我們要如何得知它和何種生物較親近 ? Ans:build a protein database,but … . Question 2: 怎麼定義 2 條蛋白質的相似度 ? Ans: Alignment techniques. Alignment. 蛋白質是由胺基酸組成的 , 所以蛋白質又可稱為胺基酸序列 序列排序 (A lignment) 的定義為分析 2 條胺基酸序列的相似度 Pairwise Alignment

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alignment

Alignment

陳致嘉

questions
Questions
  • Question 1:假設現在有1條未知的蛋白質,我們要如何得知它和何種生物較親近?
    • Ans:build a protein database,but….
  • Question 2:怎麼定義2條蛋白質的相似度?
    • Ans: Alignment techniques
alignment1
Alignment
  • 蛋白質是由胺基酸組成的,所以蛋白質又可稱為胺基酸序列
  • 序列排序(Alignment)的定義為分析2條胺基酸序列的相似度
    • Pairwise Alignment
    • Multiple sequence Alignment
compare two sequence
Compare two sequence
  • 垂直的線段”| ”表示相同的胺基酸殘基,插入缺洞(gap)而使不等長的2條序列能上下對齊
  • A simple example

SEQUENSE 1 (query) AGGVLTTQVG

| | | | | |

SEQUENSE 2 (sebject) AGGVLTQVG

SEQUENSE 1 (query) AGGVLTTQVG

| | | | | | | | |

SEQUENSE 2 (sebject) AGGVL--TQVG

compare two sequence1
Compare two sequence
  • 簡單的評分方法

[1]相同的胺基酸殘基分數+1

[2]gap分數-1

[3]extension gap get extension penalty

[4]用演算法找出分數最高的組合

  • 定義此分數為edit distance
pairwise alignment techniques
Pairwise alignment techniques
  • Question:如果我們並不想比較整條蛋白質的相似度,只想看一小段的功能呢?
    • Global alignment
    • Local alignment
use matrix
Use matrix
  • Question:在比較2條蛋白質時,有時2個不同的胺基酸殘基發生突變使得原本不同的胺基酸變成相同,該怎麼辦?
    • Ans:生物資訊上使用矩陣來分析突變的可能性
use matrix1
Use matrix
  • The Dayhoff Mutation Data Matrix

[2條蛋白質有85%以上胺基酸相等時使用]

  • The BLOSUM matrices

[2條蛋白質有85%以下胺基酸相等時使用]

the dayhoff mutation data matrix
The Dayhoff Mutation Data Matrix
  • 為一種相關機率(relatedness odds)矩陣
  • 矩陣中值大於0的元素所對應的兩個殘基之間發生突變的可能性較大
  • 值小於0的元素所對應的兩個殘基之間發生突變的可能性較小
the blosum matrices
The BLOSUM matrices?
  • The technique is almost the same!
use algorithm
Use Algorithm
  • 為求簡單,先不考慮突變的可能性,使用演算法計算2條蛋白質間的相似度
    • Global alignment

Needleman-Wunsch algorithm

    • Local alignment

Smith-Waterman algorithm

software
Software
  • FastA系列:靈敏、但是速度較慢
  • Blast系列:搜尋速度很快,但在序列相似性較低時會有失誤
multiple sequence alignment
Multiple sequence Alignment
  • 多序列排序(Multiple sequence Alignment)是對一個或多個蛋白質進行分析並將之歸類於某個基因家族
    • 作蛋白質演化分析
    • 是建立protein database的基礎
reference
Reference
  • Introduction to bioinformation

(Teresa K Attwood/David J.Parry-Smith著)

  • http://www.cs.fiu.edu /~giri/teach
  • http:// www.chinagenenet.com/commInfo