And maybe we want to model a complete intron

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Unformatted text preview: iscrimination power; maybe we want to add a more realistic six-nucleotide consensus GTRAGT at the 5′ splice site. We can put a row of six HMM states in place of ‘5’ state, to model a six-base ungapped consensus motif, parameterizing the emission probabilities on known 5′ splice sites. And maybe we want to model a complete intron, including a 3′ splice site; we just add a row of states for the 3′SS consensus, and add a 3′ exon state to let the observed sequence end in an exon instead of an intron. Then maybe we want to build a complete gene model…whatever we add, it’s just a matter of drawing what we want. The catch HMMs don’t deal well with correlations between residues, because they assume that each residue depends only on one underlying state. An example where HMMs are usually inappropriate is RNA secondary structure analysis. Conserved RNA base pairs induce long-range pairwise correlations; one position might be any residue, but the base-paired partner must be complementary. An HMM state path h...
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