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Predictive Methods Using DNA Sequences

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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  1. 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

  2. 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

  3. 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

  4. 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)

  5. 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

  6. 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

  7. 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)

  8. Promoter analysis: characterization and prediction • Pattern-driven algorithms • Sequence-driven algorithms • Prediction promoter regions

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

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