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INSTRUCTIONS This is the BIOL375 class of 2010-11. These are the students currently working with Dr. Scott on the Meiothermus ruber genome annotation project. This presentation was created by students in this course.

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This is the BIOL375 class of 2010-11. These are the students currently working with Dr. Scott on the Meiothermus ruber genome annotation project. This presentation was created by students in this course.

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Mitch Anliker, Mohammed Hussain, Heather Smith, Melissa Reller, Jose Candelario Orozco


  • Background Information on Meiothermus ruber 

  • Explain what it means to "annotate"

  •  For what Purpose?

  • Click on the speaker Icon to learn more about the Meiothermus ruber project and annotations


 What is Meiothermus ruber?

  • Procaryote:  Eubacteria domain

  • Physical characteristics:

  • Thermophile - prefers 120-140°F

  • Isolated from hot springs

  • “Pest” in paper mills

  • Non-pathogenic

  • Genome:

  • 3,000,000 base pairs

  •   *3,100 protein-coding

  •    genes predicted


  • Phylum: Thermi

  •        Class: Thermi

  •           Order: Thermales

  •                Family: Thermaceae

  •                   Genus: Meiothermus

  •                        Species: ruber

  • Pure science reasons

    • Most thermophiles belong to the Archaea domain

    • DOE’s GEBA project

    • Undergraduate research

Why study meiothermus ruber

Why study Meiothermusruber?

What is a genome annotation

What is a Genome Annotation?

A Genome Annotation is a process of attaching biological information to DNA sequences    

Why annotate more genomes



Why Annotate More Genomes?

GEBA Genomes

Genomic Encyclopedia of Bacteria & Archaea (GEBA) is a massive JGI genome sequencing effort to fill in many of the missing or under-sampled branches of the Bacteria & Archaea trees.

*T.P. Curtis, W.T. Sloan, and J.W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99: 10494-10499.

GEBA continued…

First 56 GEBA genomes* filled in several missing or under-sampled branches of the Bacteria trees & showed that there is a lot of genomic diversity out there to be discovered.

* D. Wu, P. Hugenholtz, K. Mavromatis, et al., 2009. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 462: 1056-1060.

Meiothermus ruber genome annotation project

  • Genome annotation - the process of attaching biological information to DNA sequences

    • It consists of two main steps:

      • identifying elements on the genome, a process called Gene Calling, and

      • attaching biological information to these elements

    • Technology is called Bioinformatics – using computer programs to analyze sequence information and make predictions

  • Functional genomics – benchtop research

    • Gene cloning to isolate the gene of interest from the genome

    • Mutational studies to confirm biological function predictions


M ruber g enome project

Form your argument information to DNA sequences

Large gaps in the types of bacterial genomes studied

Is there evidence to support the predictions related to my gene?

M. ruber Genome Project

Learn the tools to analyze your gene prediction

Use the tools to collect evidence to support/refute the prediction

IMG-ACT information to DNA sequences


Web Logo









Why annotate with students

Why Annotate with Students? information to DNA sequences

Most automated genome annotations - 35% are wrong

Automated annotations miss things!

 Learning new and valuable information is key

 Previous knowledge can help you!

Annotation goals

Annotation Goals information to DNA sequences

Develop and strengthen genome annotation skills such as:

Using computer programs to analyze sequence data

Gathering and evaluating information from Web-based community-accessible sequence databases

Evaluating automated gene calls

Produce quality annotations for incorporation into the Integrated Microbial Genomes Database

Build conceptual understanding of:

Evolutionary relationships among genomes

Genome organization

Power and limitations of bioinformatics

Protein structure and function

Transcriptional and translational signals

Develop basic scientific research skills such as:

Reading and evaluating primary literature

Developing hypotheses and interpreting data

Drawing conclusions from a collection of evidence

Working collaboratively

Working with real data

Img act modular annotation

IMG-ACT Modular Annotation information to DNA sequences

Streamline annotation

Emphasizes biological root of bioinformatics

More easily compatible with education

Emphasizes complementarity of tools

Allows addition and removal of modules to match student level


Module Title information to DNA sequences


Mod 1: Basic Information

DNA coordinates & base sequence, amino acid sequence, pI

Mod 2: Sequence-based Similarity Data

Sequence alignment, conserved protein domains and protein families

Mod 3: Cellular Localization Data

Signal peptide sequence, transmembrane domains


Module concepts

Module Concepts information to DNA sequences

Basic Information

Acknowledgements information to DNA sequences


Cheryl Kerfeld ([email protected])

Seth Axen ([email protected])

Microbial Genome Annotation Network:


Lori Scott, PI ([email protected])

The future is now!!! information to DNA sequences

The End!