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Unformatted text preview: Prob of Max over all prev states and state subsequence given state k durations Max ending in state j at step i-d Prob that state k has duration d Transition from j->k Courtesy of Elsevier, Inc. http://www.sciencedirect.com. Used with permission. Genscan - Burge and Karlin, (1997)
• • Explicit State Duration GHMM 5th order markov models for coding and non-coding sequences Each CDS frame has own model WAM models for start/stop codons and acceptor sites MDD model for donor sites Separate parameters for regions of different GC content Model +/- strand concurrently • • • • • Courtesy of Elsevier, Inc. http://www.sciencedirect.com. Used with permission. Types of Exons
Three types of exons are defined, for convenience: • initial exons extend from a start codon to the first donor site; • internal exons extend from one acceptor site to the next donor site; • final exons extend from the last acceptor site to the stop codon; • single exons (which occur only in intronless genes) extend from the start codon to the stop codon: Courtesy of William Majoros. Used with permission. http://geneprediction.org/book/classroom.html Intron and Exon Phase
Phase 0 Intron
Codon Phase 0 Exon 3123
Exon Intron 1231
Exon Phase 1 Intron 2312
Exon Intron Phase 1 Exon 3123
Exon Phase 2 Intron 1231
Exon Intron Phase 2 Exon 2312
Exon Two State Types in Genscan
• D-type represented by diamonds • C-type represented by circles D states are always followed by C and vice versa C states always preceded by same Dstate
Courtesy of Elsevier, Inc. http://www.sciencedirect.com. Used with permission. Two State Types in Genscan
• D-Type – geometric length distribution
– Intergenic regions – UTRs – Introns Sequence models are “factorable”: Pk ( Xa, c ) = Pk ( Xa, b) Pk ( Xb + 1, c) f k (d ) = P (state duration d|state k)=p k f k (d − 1)
Increasing duration by one changes probability by constant factor Two State Types in Genscan
• C-Type – general length distributions and sequence generating modes
– Exons (initial, internal, terminal) – Promotors – Poly-A Signals Genscan...
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This note was uploaded on 09/24/2010 for the course EECS 6.047 / 6. taught by Professor Manoliskellis during the Fall '08 term at MIT.
- Fall '08