791/7.36/BE490 Lecture 5 Mar.9.2004 Markov models 8 DNA Sequence Evolution Chris burge
7.91 / 7.36 / BE.490 Lecture #5 Mar. 9, 2004 Markov Models & DNA Sequence Evolution Chris Burge
Review of markov HMM Models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs Ch. 4 of Mount
Review of Markov & HMM Models for DNA • Hidden Markov Models - looking under the hood Ch. 4 of Mount • Markov Models for splice sites • The Viterbi Algorithm • Real World HMMs
CpG islands %C+G 60 40
CpG Islands %C+G 60 50 40 30
Cpg Island Hidden Markov Model P:=0.001 g P=0.99999 P:=0999 Genome Hidden Pn:=0.00001 Island ↓↓↓↓↓↓↓↓ A C T C GA G T A C G A T Observable CpG Island: 0.3 0.3 0.2 0.2 Genome:02020.30.3
Hidden CpG Island Hidden Markov Model P Pig = 0.001 P = 0.99999 gg ii = 0.999 Genome Pgi = 0.00001 Island … A C T C G A G T A CpG Island: C 0.3 G 0.3 A 0.2 T 0.2 Genome: 0.2 0.2 0.3 0.3 Observable
CpG Island hmm i P=0.99999 Pin =0.001 Island 99 g “ Transition Genome P:=0999 probabilities" Pn:=0.00001 ACT…℃ GA G T A C G A T “ Emission Probabilities” CpG Island:"0.3030.20.2 Genome:0.20.2030.3
CpG Island HMM II P = 0.99999 Pig = 0.001 Island gg “Transition Genome Pii = 0.999 probabilities” Pgi = 0.00001 … A C C G A G T A T CpG Island: C G A T 0.3 0.3 0.2 0.2 Genome: 0.2 0.2 0.3 0.3 “Emission Probabilities