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Greengenes: A Tutorial

Greengenes: A Tutorial. Taxonomic Classification of Bacteria Using DNA Sequences. Created by: Jonathan Davies James Logan High School Union City, CA. Background:. 1735 - Linneaus, Systema Naturae Scientific Name: Genus species

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Greengenes: A Tutorial

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  1. Greengenes: A Tutorial Taxonomic Classification of Bacteria Using DNA Sequences Created by: Jonathan Davies James Logan High School Union City, CA

  2. Background: • 1735 - Linneaus, Systema Naturae • Scientific Name: Genus species • Yesterday: Classification based on morphology, physiology & embryology • Today: Classification based on DNA • Prokaryotes can be identified/classified based on a single gene!!

  3. What is Greengenes? greengenes.lbl.gov

  4. What is Greengenes? • An up-to-date database of known 16S rRNA gene sequences • A web based tool used to classify cloned bacterial DNA sequences • Allows users to create their own local database • Allows users to compare sequences to each other and to landmarks in the Greengenes database

  5. The 16S rRNA gene • A gene found only in prokaryotes • It can be species specific - differentiating one bacterial strain from another • It codes for the small subunit of the ribosome

  6. High Throughput Analysis • A single gram of soil can contain 103-106 distinct taxa!! • Greengenes is designed to quickly and efficiently analyze large numbers of sequences (>75).

  7. Who uses Greengenes? • Clinical researchers: • To study microbes present in a patient’s throat, lungs, GI tract, etc. • Environmental microbiologists: • To compare the microbial communities from different locales • To see how a microbial community changes over time • To monitor the effectiveness of bioremediation efforts.

  8. Greengenes Tutorial Broadens target audience to include: • Advanced high school students • AP classes • Biotech classes • Science Fair projects • Undergraduate researchers

  9. Greengenes Tutorial

  10. Greengenes Tutorial • A step by step parallel to Greengenes designed to walk the user through: • Alignment of sequences to database sequences • Removal of chimeric sequences • Classification of sequences • Includes Sample Data to allow the user to test out each step on a low throughput basis • Lesson to Walk through Greengenes Using the Sample Data

  11. Teacher Resources • Lesson using sample data to gain practice with Greengenes • PowerPoint introduction for teacher and students • Sample Data to practice using Greengenes

  12. Teacher Resources • Embedded within the Tutorial are pages to cover special topics: • Point Mutations • Near Neighbors & Type Strains (for making distance trees) • Chimeras: What they are and how they’re formed. • Taxonomies: What a taxonomy is and how & why taxonomists disagree (hence Greengenes using 6 taxonomies)

  13. Future of Tutorial • Hands-on lessons to explain algorithms • Alignment • Chimeras • Taxonomies • Sample data sets to use in ecology unit • Water quality • Food poisoning • Bioremediation

  14. Acknowledgements • Todd DeSantis: Greengenes Database Administrator • Gary Andersen, PhD: PI, Molecular Microbial Ecology Group • Eoin Brodie, PhD: Microbial Ecologist • Yvette Piceno, PhD: Microbial Ecologist • Alex Butar: Bioinformatics • CSEE: Rollie Otto, Michael Thibodeau, Tom Knight • IISME: Patti Forster, Kaye Storm • Bechtel Foundation

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