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Gene Finding
7 December 11, 2000 Ron Shamir Michal Ozery-Flato and Gil Shklarski Based partially on notes taken by Benny Ben-Ami and Nadav Grossaug
Gene Finding
Motivation
Biological Background
Finding Genes in Prokaryotes
Prokaryotes
Long ORFs
Open Reading Frames (ORFs)
Finding long ORFs
Detection of Coding Regions
Codon frequencies in coding regions
ORFs as Markov chains
Using codon frequencies
Detection of Promoter Regions
RNA Transcription
E.coly
promoters
Positional Weight Matrix
Scoring Function
Promoter variation
Gene Finding in Eukaryotes
Eukaryote gene structure
Typical figures:
vertebrates
Markov Sequence Models
Splice junctions
Length Distribution
A possible Hidden Markov Model (HMM)
Exon Length Distribution
Generalized HMM
Introduction to GHMM
GenScan Model
prediction
GENSCAN
C+G Content
Initial state probabilities
Transition probabilities
State length distributions
Signal models
Performance of GENSCAN
Spliced Alignment
Definition of the spliced alignment problem
Network formulation
Spliced alignment algorithm
Improved spliced alignment algorithm
Results
Bibliography
About this document ...
Peer Itsik
2000-12-25
