MultipleAlignment

MultipleAlignment - Multiple Alignment BioE131/231 Pairwise...

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Multiple Alignment BioE131/231
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Pairwise Dynamic Programming (DP) Time O(L 2 ), memory O(L 2 )
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Three-sequence DP Time O(L 3 ), memory O(L 3 )
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Multidimensional DP Time O(L N ), memory O(L N ) Generally impractical, e.g. for globins (~99aa): Sequences Cells Memory 2 9801 40k 3 970,299 3.7M 4 96,059,601 366M 5 9,509,900,499 35G 6 9.41E+11 3.4T 7 9.32E+13 339T 8 9.28E+15 33P 9 9.14E+17 3.2E 10 9.04E+19 314E k=kilobytes M=megabytes G=gigabytes T=terabytes P=petabytes E=exabytes
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Progressive alignment Estimate a guide tree Proceed up tree, building a profile for each internal node Align siblings, going from leaves to root: Sequence-to-sequence (A-B, D-E) Sequence-to-profile (U-C) Profile-to-profile (V-W) A A B B C C D D E E U U V V W W X X A A B B C C D E E
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What’s a “profile”? A 0.8 0 0.4 0.2 1 0 C 0 0.6 0.2 0.2 0 0 G 0 0 0.4 0.4 0 0.2 T 0.2 0.4 0 0.2 0 0.8 A C A T A T A T A A A T A C G C A T T C G G A T A T C G A G Alignment Profile
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“Profile” a.k.a. “Position-specific Weight Matrix” (PWM) A 0.8 0 0.4 0.2 1 0 C 0 0.6 0.2 0.2 0 0 G 0 0 0.4 0.4 0 0.2 T 0.2 0.4 0 0.2 0 0.8
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Sequence logos Scale each column by its entropy: (technically, the difference between its entropy and the maximum possible entropy) weblogo.berkeley.edu
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Sequence logos Globin, B helix to D helix
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This note was uploaded on 12/03/2011 for the course BIO 118 taught by Professor Staff during the Fall '08 term at Rutgers.

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MultipleAlignment - Multiple Alignment BioE131/231 Pairwise...

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