Lec05-rnafold

Lec05-rnafold - CMSC 423 RNA Folding Slides By Carl Kingsford Department of Computer Science University of Maryland College Park Based on Section

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Unformatted text preview: CMSC 423: RNA Folding Slides By: Carl Kingsford Department of Computer Science University of Maryland, College Park Based on Section 6.5 of Algorithm Design by Kleinberg & Tardos. RNA Folding RNA: ACGGGGUUUAAAUUCCCUAUAT In the cell, RNA folds up: • G and C stick together • A and U stick together RNA Fold Example 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 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 { G , C } . 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 This is not allowed: i j k l In other words, if ( i , j ) and ( k ,‘ ) are paired, then we must have i < k < ‘ < j . Paired bases have to be nested . RNA Folding Problem 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 ....
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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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Lec05-rnafold - CMSC 423 RNA Folding Slides By Carl Kingsford Department of Computer Science University of Maryland College Park Based on Section

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