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Input: • Alignment. • Model parameters from neutral sequence Estimation example

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Estimation example. Input: Alignment. Model parameters from neutral sequence. Estimation example 2. HMM version. Different gene conservation patterns. Protein Coding Gene. ch10. Known non- coding gene: XIST. chX. RepA. Estimating. - PowerPoint PPT Presentation

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Page 1: Estimation example

Input:• Alignment.• Model parameters from neutral sequence

Estimation example

Page 2: Estimation example

Estimation example 2

Page 3: Estimation example

HMM version

Page 4: Estimation example

Protein Coding Gene

Known non-coding gene: XIST

ch10

chX

RepA

Different gene conservation patterns

Page 5: Estimation example

Find a ML estimator for using the EM algorithm.

Score:

Decompose Q by “extracting” the stationary distribution:

π

R: Neutral substitution pattern

: Site specific forcesπ

πEstimating

Page 6: Estimation example

Unlikeliness Score

Rate Score

Comparison

Page 7: Estimation example

43% vs 16% detection by vs.

ω π

ωπ

Proof of concept

Page 8: Estimation example

Gene and gene regulation

Page 9: Estimation example

GTACTAAGCTACTGTATGGAGGCTHuman

Mouse *****GAGC**********ATGC*

Dog *****AGGT**********CGGC*

Bat *****AGCT**********AGAC*

Find regions in the alignment whose substitution pattern is explained by the motif.

x

x

x

A generalization: Conserved motif discovery

Page 10: Estimation example

P53

MDM2

Novel non coding gene

M. Huarte, O. Zuk, M. Guttman

P53 Motif instance conservation


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