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