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Published byKya Simson Modified over 10 years ago
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Gibbs sampling Morten Nielsen, CBS, BioSys, DTU
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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
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Gibbs sampler www.cbs.dtu.dk/biotools/EasyGibbs 100 10mer peptides 2 100 ~10 30 combinations Monte Carlo simulations can do it
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Gibbs sampler. Monte Carlo simulations RFFGGDRGAPKRG YLDPLIRGLLARPAKLQV KPGQPPRLLIYDASNRATGIPA GSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEP DVFKELKVHHANENI SRYWAIRTRSGGI TYSTNEIDLQLSQEDGQTIE RFFGGDRGAPKRG YLDPLIRGLLARPAKLQV KPGQPPRLLIYDASNRATGIPA GSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEP DVFKELKVHHANENI SRYWAIRTRSGGI TYSTNEIDLQLSQEDGQTIE E1 = 5.4 E2 = 5.7 E2 = 5.2 P accept =1 0 < P accept < 1
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Monte Carlo Temperature What is the Monte Carlo temperature? Say dE=-0.2, T=1 T=0.001
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Shift alignment window Gibbs sampler. Monte Carlo simulations Getting stucked in local minima
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It works High TemperatureLow Temperature
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Gibbs sampler. Prediction accuracy
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Use of Gibbs sampling More than 1,000 papers in PubMed using Gibbs sampling methods Transcription start-sites Receptor binding sites Acceptor:Donor sites...
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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
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