Joint and marginal probabilities Joint: Marginal: How to compute - PowerPoint PPT Presentation

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Joint and marginal probabilities Joint: Marginal: How to compute the probability of observations Forward algorithm Forward algorithm Forward algorithm Decoding: finding the most probable states Similar to the forward algorithm, we can define

Joint and marginal probabilities Joint: Marginal:
How to compute the probability of observations
Forward algorithm
Forward algorithm
Forward algorithm
Decoding: finding the most probable states Similar to the forward algorithm, we can define the following value:
Viterbi algorithm
Gene finding
Gene finding
Gene finding • In human genome, ~3% of DNA sequence is genes • Lot of “junk” DNA between genes, and even inside genes (between exons). • Due to the reverse complement, one gene can start from either direction. • Gene finding must deal with these.
Gene finding for bacterial genomes In bacteria, there is no intron in the coding region.
Gene finding for bacterial genomes In bacteria, there is no intron in the coding region. start state stop state Codon usage can be different between the noncoding regions and coding regions.
Gene finding for bacterial genomes Horizontal gene transfer Codon usages can be different in the typical coding regions and the atypical coding regions.
Gene finding: frames
Gene finding: HMM for bacteria GeneMarker’s HMM model
Gene finding: handling introns
Gene finding: handling introns Splicing site motifs
Gene finding: handling introns Splicing site motifs
Gene finding: HMM version 2

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