Pairwise Sequence alignment Query: catcaactacaactccaaagacaccctyaFacccactaggatatcaacaa |||||||| l|||||||||||||||| Sbjct: catcaactgcaaccccaaagccacccct-Facccactaggatatcaacaa 插入gap Multiple sequence alignment EIQDVSGTWYAMTVDREFPEMNLESVTPMTLTTL. GGNLEAKVTM LSFTLEEEDITGTWYAMVVDKDFPEDRRRKVSPVKVTALGGGNLEATFTE TKQDLELPKLAGTWHSMAMATNNISLMATLKAPLRVHITSEDNLEIVLHR VQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGNQELRADGTV VKEN FDKARFSGTWYAMAKDPEGLFLQDNIVAEFSVDETGNWDVCADGTF LQQNFQDNQFQGKWYVVGLAGNAI. LREDKDPQKMYATIDKSYNVTSVLF VQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVDGGLNLTSTFL VQENENISRIYGKWYNLAIGSTCPWMDRMTVSTLVLGEGEAEISMTSTRW PKANFDAQQFAGTWLLVAVGSACRFLQRAEATTLHVAPQGSTFRKLD
▪ Pairwise Sequence Alignment Query: catcaactacaactccaaagacacccttacacccactaggatatcaacaa |||||||| |||| |||||| ||||| | ||||||||||||||||||||| Sbjct: catcaactgcaaccccaaagccacccct-cacccactaggatatcaacaa ▪ Multiple Sequence Alignment -----EIQDVSGTWYAMTVDREFPEMNLESVTPMTLTTL.GGNLEAKVTM LSFTLEEEDITGTWYAMVVDKDFPEDRRRKVSPVKVTALGGGNLEATFTF TKQDLELPKLAGTWHSMAMATNNISLMATLKAPLRVHITSEDNLEIVLHR VQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGNQELRADGTV VKENFDKARFSGTWYAMAKDPEGLFLQDNIVAEFSVDETGNWDVCADGTF LQQNFQDNQFQGKWYVVGLAGNAI.LREDKDPQKMYATIDKSYNVTSVLF VQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVDGGLNLTSTFL VQENFNISRIYGKWYNLAIGSTCPWMDRMTVSTLVLGEGEAEISMTSTRW PKANFDAQQFAGTWLLVAVGSACRFLQRAEATTLHVAPQGSTFRKLD... 插入gap
双序列比对打分 口序列1: V D S 门序列2: Vs工cY J match/mismatch pair score: 4 2 4 97 gaps penalty: 口两序列比对的总分: Score =2(Aa pair scores)-gap penalty 4+2+4+9+7-11 15 Genomics and Bioinformatics 2015. TMML
Genomics and Bioinformatics 2015, TMMU 双序列比对打分 序列1： V D S – C Y 序列2： V E S L C Y match/mismatch pair score：4 2 4 9 7 gaps penalty： -11 两序列比对的总分： Score = Σ(AA pair scores) – gap penalty = 4+2+4+9+7-11 = 15
氨基酸打分矩阵: BLOSUM D BLOSUM: BLOcks sUbstitution matrix G0-20-1 -2-26 BLOSUM62打分矩阵 -3-4-324 2-1-3|-25 00 P|-1-2-2-1-3-1 -2-2-3-3 R DCQEGH L KMFP Genomics and Bioinformatics 2015. TMMU
Genomics and Bioinformatics 2015, TMMU 氨基酸打分矩阵：BLOSUM BLOSUM：BLOcks SUbstitution Matrix A 4 R -1 5 N -2 0 6 D -2 -2 1 6 C 0 -3 -3 -3 9 Q -1 1 0 0 -3 5 E -1 0 0 2 -4 2 5 G 0 -2 0 -1 -3 -2 -2 6 H -2 0 1 -1 -3 0 0 -2 8 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 K -1 2 0 -1 -1 1 1 -2 -1 -3 -2 5 M -1 -2 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 A R N D C Q E G H I L K M F P S T W Y V BLOSUM62打分矩阵
An example of pairwise alignment of an unknown protein with a known one (A) Glutaredoxin(谷氧还蛋白, Bacteriophage T4fomE.co,87aa (B)Unknown protein, Bacteriophage 65 from Aeromonas sp 93 aa 10 20 30 40 50 Glutar KVYGYDSNIHKCVYCDNAKRLLTVKKQPFEFINIMPEKGV---FDD-EKIAELLTKLGR Unknow EIYGIPEDVAKCSGCI SAIRLCFEKGYDYEIIPVLKKANNQLGEDYILEKFDECKARANM 10 20 30 40 50 60 60 70 80 Glutar DTQIGLTMPQVEAPDGSHIGGFDOLREYF Unknow QTR-PTSFPRIFV-DGQYIGSLKQFKDLY Is the unknown protein 70 80 90 a glutaredoxin?
19 An example of pairwise alignment of an unknown protein with a known one (A) Glutaredoxin (谷氧还蛋白), Bacteriophage T4 from E. coli, 87 aa (B) Unknown protein - 93 aa 10 20 30 40 50 Glutar KVYGYDSNIHKCVYCDNAKRLLTVKKQPFEFINIMPEKGV---FDD—EKIAELLTKLGR ..:: .. :: : .: :: : .:.: .. . . :: ::. : .. . Unknow EIYGIPEDVAKCSGCISAIRLCFEKGYDYEIIPVLKKANNQLGFDYILEKFDECKARANM 10 20 30 40 50 60 60 70 80 Glutar DTQIGLTMPQVFAPDGSHIGGFDQLREYF .:. ..:..:. ::..::.. :... . Unknow QTR-PTSFPRIFV-DGQYIGSLKQFKDLY 70 80 90 Is the unknown protein a glutaredoxin? Unknown protein, Bacteriophage 65 from Aeromonas sp. 93 aa
全局比对和局部比对 门全局比对( Global alignment) 在整个序列比对,适于长度和相似性较高的 序列 ●全局比对算法: Needleman- Wunsch,1970 口局部比对( Local alignment): e在一段区城比对,适于差异较多的序列 ●局部比对算法:Smth- Waterman,1981 Genomics and Bioinformatics 2015. TMML
Genomics and Bioinformatics 2015, TMMU 全局比对和局部比对 全局比对（Global Alignment）： 在整个序列比对，适于长度和相似性较高的 序列 全局比对算法：Needleman-Wunsch，1970 局部比对（Local Alignment）： 在一段区域比对，适于差异较多的序列 局部比对算法：Smith-Waterman，1981