Discover Regulatory Modules Consisting

1
Discover Regulatory Modules Consisting of
Multiple Binding Sites
Student YunJun Lai
Advisor Yuh-Jyh Hu

• New Features of SAMAL
• No pre-defined Background.
• Modeling Motif.
• Modeling Distance Relation between Motifs.
• The NEW module scoring function derive form
  bayesian inference.

Sequences with combinatorial motifs.
Regulatory Module
G input sequences li length of i-th
sequence gi(p) the nucleotide at position
p at i-th sequence
Motif
Distance

T
G
,
A module start indicator
Background
D distance recorder
Background
T motif model
GCATGATCGATACGTCATTTATACGATCGAGTATCAATCAGTCGATGATC
TA
G distance model
P(distance7) G(7)
Predicted Site
Transcription Factor
Real Binding Site
14,15
rpoH
Two kernel motifs with gaps14.
Two kernel motifs with gaps13.
CRP
cpxR