lect 11 pairwise alignment

# lect 11 pairwise alignment - Bioc 2808 Lecture 11 Pairwise...

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Click to edit Master subtitle style 7/29/10 Bioc 2808 Lecture 11 Pairwise alignments Instructor Dr. Junwen Wang

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7/29/10 Motivation Why align two protein or DNA sequences? Determine whether they are descended from a common ancestor (homologous). Infer a common function. Locate functional elements (motifs or domains). Infer protein structure, if the structure of one of the sequences is known.
7/29/10 Sequence comparison overview Problem: Find the “best” alignment between a query sequence and a target sequence. To solve this problem, we need a method for scoring alignments, and an algorithm for finding the alignment with the best score. The alignment score is calculated using a substitution matrix, and gap penalties.

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7/29/10 GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLP G F+ G CP +FD+ + G W+EI K+P GQNFHLGKCPSPPVQENFDVKKYLGRWYEIEKIP LENENQGKCTIAEYKYDGKKASVYNSFVSNGVKE E +G C A Y S + NG E ASFE-KGNCIQANY-----------SLMENGNIE YMEGDLEIAPDAKY------TKQGKYVMTFKFGQ + D E++PD KQ K VL--DKELSPDGTMNQVKGEAKQSNVSEPAKLEV RVVNLVP----WVLATDYKNYAINYNCD-----Y + L+P W+LATDY+NYA+ Y+C + QFFPLMPPAPYWILATDYENYALVYSCTTFFWLF HPDKKAHSIHAWILSKSKVLEGNTKEVVDNVLKT H D WIL ++ L T + ++L HVD------FFWILGRNPYLPPETITYLKDILT- Y mutates to V receives -1 M mutates to L receives 2 E gets deleted receives -10 G gets deleted receives -10 D matches D receives 6 Total score = -13
7/29/10 Two kinds of sequence alignment: We will first consider the global alignment algorithm of Needleman and Wunsch (1970). We will then explore the local alignment algorithm of Smith and Waterman (1981). Finally, we will consider BLAST, a heuristic version of Smith-Waterman.

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7/29/10 Needleman and Wunsch Algorithm (1970) Two sequences can be compared in a matrix along x- and y-axes. If they are identical, a path along a diagonal can be drawn. Find the optimal subpaths, and add them up to achieve the best score. This involves adding gaps when needed
7/29/10 A simple alignment problem. Problem: find the best pairwise alignment of GAATC and CATAC .

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7/29/10 Scoring alignments We need a way to measure the quality of a candidate alignment. Alignment scores consist of two parts: a substitution matrix , and a GAATC CATAC GAATC- CA-TAC GAAT-C C-ATAC GAAT-C CA-TAC -GAAT-C C-A-TAC GA-ATC CATA-C
Scoring aligned bases Purine A G Pyrimidine C T Transition (high score) Transversi on (low score)

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7/29/10 Scoring aligned bases Purine A G Pyrimidine C T Transitio n Transversi on A C G T A 10 -5 0 -5 C -5 10 -5 0 G 0 -5 10 -5 T -5 0 -5 10 A hypothetical substitution matrix: GAATC CATAC -5 + 10 + -5 + -5 + 10 = 5
7/29/10 A R N D C Q E G H I L K M F P S T W Y V B Z X A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1

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lect 11 pairwise alignment - Bioc 2808 Lecture 11 Pairwise...

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