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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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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.

You will need speakers or a headset to hear the narration attached to this presentation.

On most pages, you will see a speaker icon like this one . Click on the icon to hear the narration. When finished with one slide, click “enter” to advance to the next slide.


MEIOTHERMUS RUBER

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


Introduction

  • 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


BACKGROUND

 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


  • BACKGROUND CONTINUED

  • 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

Bacteria

Archaea

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

MEIOTHERMUS RUBER GENOME ANNOTATION PROJECT


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

TMHMM

Web Logo

T-Coffee

BLAST

SignalP

NCBI

KEGG

TIRGfam

Phobius

Phylogeny.fr

PSORT


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


Annotation

Module Title information to DNA sequences

Description

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

ANNOTATION


Module concepts

Module Concepts information to DNA sequences

Basic Information


Acknowledgements information to DNA sequences

IMG-ACT (JGI):

Cheryl Kerfeld ([email protected])

Seth Axen ([email protected])

www.jgi.doe.gov/education/annotation_tools.html

Microbial Genome Annotation Network:

(NSF RCN-UBE)

Lori Scott, PI ([email protected])

mgan.jgi-psf.org


The future is now!!! information to DNA sequences

The End!