SequenceAlignment-Application-Lirq课件.ppt

– the foundation of bioinformatics analysis 李瑞强 lirq@ Beijing Genomics Institute 2006-03-17 Sequence alignment 持彻宜脂蔼絮撑奴激科优隧兆肄之毡寇矮忿澡恤谦妈胚岔驼灾锯踊交凭扼SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 Types of Alignment - Algorithm Dot Plots Dynamic programing (blast, fasta) Global - Needelman-Wunsch Local - Smith-Waterman Profile based (HMM, Psi-blast) Structure based - Object DNA  DNA DNA  Protein Protein  Protein Protein  Structure Structure  Structure 盾奶可者弟掐兄奖贝钳滥喉嚎滚桔沸豌诊龚卉缨良茁咏寨姑汀玛俱乏福叫SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 Dot Plot – the simplest way to visualize pair-wise alignment Put a dot in the cell (i,j) if character in row i is the same as in column j, A(i) = A(j). 稗嗡起偿二铜堪汲互彼歹盎卜拢沃崇咐霍爸比篮没郸瓤混吮褐营赏坷喀毁SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 Dynamic programing in equation form Align sequence x and y. F is the DP matrix; s is the substitution matrix; d is the linear gap penalty. 力邯裳整扎毫贮絮流装宽襄拱乱臃礼眺养搓巳富灵同哑蛹然卑窜灰姨鼻侧SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 DP in equation form 湃龋刁陷拐知尽转涧韶拳姓械首缘卷搁咕撵孩狞毕涪汉盆袋挝才圈滚赋廷SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 A simple example A C G T A 2 -7 -5 -7 C -7 2 -7 -5 G -5 -7 2 -7 T -7 -5 -7 2 A A G A G C Find the optimal alignment of AAG and AGC. Use a gap penalty of d=-5. 樊淤梧扔馅草尘诫帜卑撑卞甜淌坡峡工户催鸟蹲矾廊技淌逐抵噪潮遇织质SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 A simple example A C G T A 2 -7 -5 -7 C -7 2 -7 -5 G -5 -7 2 -7 T -7 -5 -7 2 A A G 0 A G C Find the optimal alignment of AAG and AGC. Use a gap penalty of d=-5. 戌捆昂始也把隔蓟徘铜历多葱佐钨誉孺睫案皇无助破谴亿菊溜彬卿昭诲藕SequenceAlignment-Application-Lirq课件SequenceAlignment-Application-Lirq课件 A simple example A C G T A 2 -7 -5 -7 C -7 2 -7 -5 G -5 -7 2 -7 T -7 -5 -7 2 A A G 0 -5 -10 -15 A -5 G -10 C -15 Find the optimal alignment of AAG and AGC. Use a gap penalty of d=-5. 肌油妻杭祷剧状淬澡朝箍脐烫臣奸叮碘试墨蚀涧廉录用榷且誓饼莲惟泣琢SequenceAlignment-