“A structure based flexible search method for motifs in RNA” Isana ...

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2. Tree Inclusion T1 is included in T2 if there is a sequence of delete operations performed on T2 which makes T2 isomorphic to T1. The tree inclusion problem is to decide if T1 is included in T2.
� Polynomial time algorithms exist for these problems. They are all based on the classical technique of dynamic programming and most of them are simple combinatorial algorithms.
Page 1 and 2: STRMS “A structure based flexible
Page 3 and 4: The Central Dogma of DNA transcript
Page 5 and 6: Non Coding RNA Families �They are
Page 7 and 8: Our Goal Discover ncRNA motifs in a
Page 9 and 10: Our method consists of two phases:
Page 11 and 12: RNA’s Secondary Structure (((((((
Page 13 and 14: Ordered rooted tree Shapiro, 1988:
Page 15 and 16: Our tree representation origin of a
Page 17 and 18: Comparison of ordered rooted trees
Page 19 and 20: 1. Edit distance � An edit script
Page 21 and 22: 1. Edit distance
Page 23 and 24: 1. Edit distance
Page 25: 2. Tree Inclusion T1 is included in
Page 29 and 30: The Algorithm � The subtree isomo
Page 31 and 32: The Algorithm - Motivation � In s
Page 33 and 34: Subtree Homeomorphism Score � Giv
Page 35 and 36: The Tree Alignment Algorithm � A
Page 37 and 38: The two-stage DP approach to the tr
Page 39 and 40: Dealing with Potential Pseudoknots
Page 41 and 42: Updating the S DP X : pseudoknot in
Page 43 and 44: Experimental Results � Riboswitch
Page 45 and 46: Purine Riboswitch The secondary str
Page 47 and 48: Results - Second dataset � The se
Page 49: Searching for riboswitches in newly

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