1 / 13

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.

tirza
Download Presentation

Predictive Methods Using DNA Sequences

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related