Michal Ziv-Ukelson Comparative Structural RNAomics (Pattern Matching on Strings,
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Michal Ziv-Ukelson
Comparative Structural RNAomics (Pattern Matching on Strings ,
(and Graphs Trees
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Context Fold
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Context Fold
• Applied machine learning algorithms over large datasets of solved structures
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ACGCUGACGUAGUCAGUAGACGACAGACAGAUACGUCACCGCAGAUACGCAUAGUAGCAGUAGCAGAUGACGACGCUGACGUAGUCAGUAGACGACAGACAGAUACGUCACCGCAGAUACGCAUAGUAGCAGUAGCAGAUGACG…………………………………………………………………………………………
Genome SequenceQUERY
Are there any appearances of this structure in the genome?
RNA Structural Search 1(STRMS)
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ACGCUGACGUAGUCAGUAGACGACAGACAGAUACGUCACCGCAGAUACGCAUAGUAGCAGUAGCAGAUGACGACGCUGACGUAGUCAGUAGACGACAGACAGAUACGUCACCGCAGAUACGCAUAGUAGCAGUAGCAGAUGACG…………………………………………………………………………………………
Genome Sequence millions of nucleotidesQUERY
Are there any appearances of sequences that fold similarly to
this sequence in the genome?
RNA Structural Search 2 (Stem Search)
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B
C
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ON CLIC
K
B
C
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Stem Search
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Results
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Results
dashed arrows - validated targets
solid green arrows - new regulation patterns discovered in our module