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Predictive Methods Using DNA Sequences PowerPoint PPT Presentation


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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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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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  • 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


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  • 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


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  • 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)


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  • 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


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  • 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


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  • 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)


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  • Promoter analysis: characterization and prediction

    • Pattern-driven algorithms

    • Sequence-driven algorithms

    • Prediction promoter regions


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http://biology200.gsu.edu/houghton/4564%20'04/lecture10.html


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