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Predictive Methods Using DNA Sequences

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Predictive Methods Using DNA Sequences. 5.1 Introduction 5.2 Gene prediction methods 5.3 Gene prediction programs 5.4 How well do the methods work? 5.5 Promoter analysis: characterization and prediction 5.6 Strategies and considerations 5.7 Visualization and tergration tools 5.8 Summary.

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Presentation Transcript
slide1

Predictive Methods Using DNA Sequences

  • 5.1 Introduction
  • 5.2 Gene prediction methods
  • 5.3 Gene prediction programs
  • 5.4 How well do the methods work?
  • 5.5 Promoter analysis: characterization and prediction
  • 5.6 Strategies and considerations
  • 5.7 Visualization and tergration tools
  • 5.8 Summary
slide2
Gene prediction method
    • Searching by signal
    • Searching by content: compositional, coding region
    • Homology-based gene prediction
    • Comparative gene prediction
    • ab initio gene prediction (intrinsic or template prediction)
    • Extrinic, look-up gene prediction
    • Prokaryotes vs eukaryotes
slide3
Prokaryotes gene prediction
    • Web server
      • NCBI ORF finder
      • GeneMark
      • Softberry
      • Easy gene
    • Upstream
      • Ribosome binding site (GA rich) sequences
      • Promoter region
    • Downstream
      • Terminator- Rho dependent stem-loop structure
slide4
Eukaryotes gene prediction
    • Identifying suitable splice and start and stop signals
    • Predicting exons
    • Assembling
  • Prediction of exon-defining signals
    • Translation start site
    • 5’ splice site
    • 3’ splice site
    • Translation stop codon
    • Position weight matrices (PWMs)
slide5
Prediction and Scoring of exons
    • Depends on content-based features
    • Initial exons: ORFs delimited by a start site and a 5’ site
    • Internal exons: ORFs delimited by a 3’ site and a 5’ site
    • Terminal exons: ORFs delimited by a 3’ site and stop codon
    • Protein-coding regions from noncoding regions
slide6
Prediction of genes through ab initio method
    • Hidden Markov model (HMMs)
      • Genscan
      • Genie
      • HMMgene
  • Sequence similarity-based gene prediction
    • BLASTX search useful in prokaryote
    • Novel approach: BLASTX + initio
      • genomeScan
      • GeneID
    • EST: expressed sequence tag for BLAST
      • Viable ORF is not identified
      • GRAIL-EXP: use splice site models
slide11
Comparative gene prediction
    • Complete genomes available
      • TWINSCAN (extension GENSCAN)
      • SGP-2 (GenID)
      • SLAM (HMM-based)
  • Gene prediction programs (AY292986)
    • GRAIL (gene recognition and analysis internet link)- GRAIL2, GRAIL-EXP
    • GeneID:
    • GENSCAN: MIT
    • FGENES: softberry.com
    • GENEWISE: EBI-tools (protein structure)
slide12
Promoter analysis: characterization and prediction
    • Pattern-driven algorithms
    • Sequence-driven algorithms
    • Prediction promoter regions
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