INSTRUCTIONS

1. 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.

2. MEIOTHERMUS RUBER Mitch Anliker, Mohammed Hussain, Heather Smith, Melissa Reller, Jose Candelario Orozco

3. 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

4. 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

5. 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

6. Practical reasons • Contaminant of paper mills • Contains an enzyme that digests feathers Why study Meiothermusruber?

7. What is a Genome Annotation? A Genome Annotation is a process of attaching biological information to DNA sequences    

8. Bacteria Archaea Why Annotate More Genomes?

9. 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.

10. 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.

11. 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

12. Form your argument 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

13. IMG-ACT TMHMM Web Logo T-Coffee BLAST SignalP NCBI KEGG TIRGfam Phobius Phylogeny.fr PSORT

14. Why Annotate with Students? Most automated genome annotations - 35% are wrong Automated annotations miss things!  Learning new and valuable information is key  Previous knowledge can help you!

15. Annotation Goals 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

16. IMG-ACT Modular Annotation 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

17. Module Title 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

18. Module Concepts Basic Information

19. Acknowledgements IMG-ACT (JGI): Cheryl Kerfeld (ckerfeld@lbl.gov) Seth Axen (saxen@lbl.gov) www.jgi.doe.gov/education/annotation_tools.html Microbial Genome Annotation Network: (NSF RCN-UBE) Lori Scott, PI (LoriScott@augustana.edu) mgan.jgi-psf.org

20. The future is now!!! The End!