michal ziv-ukelson comparative structural rnaomics (pattern matching on strings,

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