MIT6_047f08_lec08_slide08

Httpwwwsciencedirectcom used with permission genscan

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

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...
View Full Document

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.

Ask a homework question - tutors are online