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

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Outline � Background � Motivation � RNA’s structure representations � Trees comparison � Our Algorithm � Results
The Central Dogma of DNA transcription RNA translation Protein Molecular Biology Non Coding RNA - RNA molecule that is not translated into a protein - Have been found to have roles in a great variety of processes DNA RNA Protein
Page 1: STRMS “A structure based flexible
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 and 26: 2. Tree Inclusion T1 is included in
Page 27 and 28: � Polynomial time algorithms exis
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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