生物信息學(xué)序列比對(duì)課件

1、Sequence Analysis (II)Sequence AlignmentGalacid-Secret of LifeNucleicAcidsA T(U) G CProteins20 amino acidsSalvador Dalis Galacidalacidesoxyribonucleicacid, Homage to Watson and Crick, 1963. Note the figures in quartets to the right signifying the tetranucleotide hypothesis that DNA was composed of a

2、 simple repeating unit of A, C, G and T and was therefore too simple to encode genetic information an idea that was obsolete even by the time Dali painted Galacid.Whats Alignment3The Need of Sequence AlignmentHomology study 同源研究Phylogenetic study系統(tǒng)進(jìn)化研究Pattern (motif) identification 模式識(shí)別Protein Famil

3、y Classification家族分類EST analysis 表達(dá)序列標(biāo)簽分析Gene Identification 基因識(shí)別Genomic study 組學(xué)研究Protein-Protein Interaction 蛋白相互作用More4Principle of Sequence Alignment序列比對(duì)原理DotplotsPairwise alignmentLocal alignmentGlobal alignmentMultiple alignmentDotplotsNeedleman/Wunsch/SellersSmith/WatermanGotohSpliced and mor

4、eWhats Alignment同源序列、相似序列和相同序列相似序列的定量描述Seq-a: ATC ACCTT GGTAGCTASeq-b: TAC ACCTT CGTCGCCA打分規(guī)則1（相同記為1，不同記為0） 1 + 5 + 5 = 11打分規(guī)則2（相同記為0.8，不同記為0.2） 1.2 + 4 + 4.6 = 9.8打分規(guī)則3 -3 + 25 + 13 = 35ATCGA5-4-4-4T-45-4-4C-4-45-4G-4-4-45Simple Score Scheme最簡(jiǎn)單的打分規(guī)則匹配：+5分不匹配：0分舉例：肽鏈A：K A W S A D V肽鏈B：K D W S A E V5

5、+0+5+5+5+0+5=25對(duì)于核酸序列仍然適用替換和突變突變：DNA的復(fù)制和修復(fù)過(guò)程中出現(xiàn)錯(cuò)誤而導(dǎo)致的核苷酸序列的改變替換：經(jīng)過(guò)自然選擇過(guò)濾后保留下來(lái)的突變同義和異義替換：甘氨酸：GGG, GGA, GGU, GGC編碼基因的序列發(fā)生同義替換的概率差不多是異義替換的3倍人/鼠同義替換率異義替換率生長(zhǎng)激素0.3210.100載脂蛋白E0.1990.148組蛋白(H2A)0.9670.057估計(jì)替換數(shù)目核酸序列之間的差異可以用替換數(shù)目（K）表示如果序列之間的差異很大，K有可能被低估Jukes-Cantor模型：K=-3/4ln1-(4/3(p)Kimura雙參數(shù)模型：K=1/2ln1/(1-2

6、P-Q)+1/4ln1/(1-2Q)多參數(shù)模型：誤差太大 時(shí)刻0 時(shí)刻1 時(shí)刻2位點(diǎn) C T C轉(zhuǎn)換和顛換Conserved Substitution氨基酸的保守替換Substitution of S/T or E/D should result in scores that are only moderately lower than identities. A.A. have similar physicochemical properties can be replaced each other such as Serine (S) & Threonine (T), Aspartic a

7、cid (D) & Glutamic acid (E)各種不同的替換計(jì)分矩陣4種堿基，20種氨基酸各種堿基或氨基酸的理化性質(zhì)不同各種突變發(fā)生的概率不同DNA記分矩陣：等價(jià)矩陣、轉(zhuǎn)換-顛換矩陣、BLAST矩陣蛋白質(zhì)記分矩陣：等價(jià)矩陣、遺傳密碼矩陣、疏水性矩陣、PAM矩陣BLOSUM矩陣來(lái)源于對(duì)自然界氨基酸替換概率的統(tǒng)計(jì)PAM-1Protein substitution matrices蛋白替換矩陣BLOSUM250 matrix: Positive scores on diagonal(identities) Similar residues get higherscores Dissimila

8、r residues getsmaller (negative) scores怎樣選用PAM-n和BLOSUM-n矩陣PAM矩陣：n越小表示氨基酸變異的可能性越小BLOSUM矩陣：n越小表示氨基酸相似的可能性越小BLOSUM 80PAM 1序列相似度高BLOSUM 45PAM 250序列相似度低BLOSUM 62PAM 120什么是Gap空格 (gap)Seq-a: ATACCTTGGTAGCTASeq-b: ATGACCTTGGTAGCTASeq-a: AT-ACCTTGGTAGCTASeq-b: ATGACCTTGGTAGCTA突變位點(diǎn)上的替換、插入和刪除引起了序列的差異Gap Penal

9、ty空位罰分Multiple insertions/deletions may be one evolutionary eventSeparate penalties for gap opening and gap elongationK L A A S V I L S D A LK L A A - - - - S D A L-10 + 3 x (-1)=-13起始罰分長(zhǎng)度罰分利用點(diǎn)矩陣進(jìn)行序列比對(duì)Dotplots AlgorithmDotplots two sequecne (x, y)length(x) = MLength(y) = Nfor i = 1- Mfor j = 1 - Nif

10、 xi = yjD(i, j) = 1elseD(i, j) = 0O(MN)Dynamic Programming動(dòng)態(tài)規(guī)劃法求解序列比對(duì)問(wèn)題分解序列1： ACTCG序列2： ACAGTAG第一位點(diǎn)得分剩余序列AA+1CTCGCAGTAG-A-1ACTCGCAGTAGA-1CTCGACAGTAGDynamic Programming動(dòng)態(tài)規(guī)劃法求解序列比對(duì)序列1： ACTCG序列2： ACAGTAGgapACTCGgap0-1-2-3-4-5A-110-1-2-3C-20210-1A-3-11210G-4-20122T-5-3-1112A-6-4-2011G-7-5-3-102多重序列比對(duì)Mul

11、tiple sequence alignment動(dòng)態(tài)規(guī)劃法：n條序列 n維矩陣ClustalW、ClustalX和ClustalO多序列比對(duì)的應(yīng)用獲得共性序列（Consensus sequence）序列測(cè)序突變分析種系分析保守區(qū)段分析基因和蛋白質(zhì)功能分析Alignment exercise獲取HBV A、B、C、D亞型參考序列（HBV genotype A/B/C/D）訪問(wèn)EMBOSS和MobylePasteur，利用比對(duì)工具比對(duì)四條序列訪問(wèn)Clustal: Multiple Sequence Alignment網(wǎng)站下載ClustalX和ClustalO，比對(duì)4條序列Homework下載HPV 16/1