423f11-rnafold

423f11-rnafold - RNA Folding CMSC 423 Lecture by Darya Filippova RNA Folding G C C G U A A U U A C G C G A U A U G G G U A A A A G C C G G C U U A

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Unformatted text preview: RNA Folding CMSC 423 Lecture by Darya Filippova RNA Folding G C C G U A A U U A C G C G A U A U G G G U A A A A G C C G G C U U A A A G A C C G G U C U U U A C C C C G G A U A U G C C C C A A RNA is single stranded and folds up: • G and C stick together • A and U stick together RNA Folding Rules RNA folding rules: 1. If two bases are closer than 4 bases apart, they cannot pair 2. Each base is matched to at most one other base 3. The allowable pairs are {U, A} and {C, G} 4. Pairs cannot “cross.” G C C G U A A U U A C G C G A U G C C G U A A U U A C G C G A U No Crossings If ( i , j ) and ( k , m ) are paired, we must have i < k < m < j. Paired bases have to be nested. i j k m RNA Folding Given : a string r = b 1 b 2 b 3 ,..., b n with b i ∈ {A,C,U,G} Find : the largest set of pairs S = {( i , j )}, where i,j ∈ {1,2,..., n } that satisfies the RNA folding rules . Goal: match as many bases as possible. Subproblems G C C G U U A U U A C G C G A U 1 j G C C G U U A U U A C G C G A U 1 j j is not paired with anything j is paired with some t ≤ j -4 t OPT(t+1, j-1) OPT(1, t-1) OPT(1, j-1) Recurrence If j- i ≤ 4: OPT ( i, j...
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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423f11-rnafold - RNA Folding CMSC 423 Lecture by Darya Filippova RNA Folding G C C G U A A U U A C G C G A U A U G G G U A A A A G C C G G C U U A

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