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Gibbs sampling
Morten Nielsen,CBS, BioSys,
DTU
Class II MHC binding
• MHC class II binds peptides in the class II antigen presentation pathway• Binds peptides of length 9-18 (even whole proteins can bind!)• Binding cleft is open• Binding core is 9 aa
Gibbs samplerwww.cbs.dtu.dk/biotools/EasyGibbs
100 10mer peptides2100~1030 combinations
Monte Carlo simulations can do
it
Gibbs sampler. Monte Carlo simulations
RFFGGDRGAPKRGYLDPLIRGLLARPAKLQVKPGQPPRLLIYDASNRATGIPA GSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEPDVFKELKVHHANENI SRYWAIRTRSGGITYSTNEIDLQLSQEDGQTIE
RFFGGDRGAPKRGYLDPLIRGLLARPAKLQVKPGQPPRLLIYDASNRATGIPAGSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEPDVFKELKVHHANENI SRYWAIRTRSGGITYSTNEIDLQLSQEDGQTIE
E1 = 5.4 E2 = 5.7
E2 = 5.2
Paccept =1
0 < Paccept < 1
Monte Carlo Temperature
• What is the Monte Carlo temperature?
• Say dE=-0.2, T=1
• T=0.001
Shift alignment window
Gibbs sampler. Monte Carlo simulations
Getting stucked in local minima
It works
High Temperature Low Temperature
Gibbs sampler. Prediction accuracy
Use of Gibbs sampling
• More than 1,000 papers in PubMed using Gibbs sampling methods• Transcription start-sites• Receptor binding sites• Acceptor:Donor sites• ...
Summary
• Weight matrices can accurately describe a sequence motif like MHC class I• Use sequence weighting to remove data
redundancy• Use pseudo count to compensate for few
data points
• Gibbs sampling can detect MHC class II binding motif