2. 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.

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

4. 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

5. 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

6. 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

7. W HY STUDY M EIOTHERMUS RUBER ? Practical reasons Contaminant of paper mills Contains an enzyme that digests feathers

8. W HAT IS A G ENOME A NNOTATION ? A Genome Annotation is a process of attaching biological information to DNA sequences

9. W HY A NNOTATE M ORE G ENOMES ? Archaea Bacteria

10. GEBA Genomes *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. 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.

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

12. MEIOTHERMUS RUBER GENOME ANNOTATION PROJECT Genome annotation - the process of attaching biological information to DNA sequences o It consists of two main steps:  identifying elements on the genome, a process called Gene Calling, and  attaching biological information to these elements o Technology is called Bioinformatics – using computer programs to analyze sequence information and make predictions Functional genomics – benchtop research o Gene cloning to isolate the gene of interest from the genome o Mutational studies to confirm biological function predictions

13. M. RUBER G ENOME P ROJECT Is there evidence to support the predictions related to my gene? Large gaps in the types of bacterial genomes studied Learn the tools to analyze your gene prediction Use the tools to collect evidence to support/refute the prediction Form your argument

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

15. W HY A NNOTATE WITH S TUDENTS ? Most automated genome annotations - 35% are wrong Automated annotations miss things! Learning new and valuable information is key o Previous knowledge can help you!

16. A NNOTATION G OALS Develop and strengthen genome annotation skills such as: o Using computer programs to analyze sequence data o Gathering and evaluating information from Web-based community- accessible sequence databases o Evaluating automated gene calls Produce quality annotations for incorporation into the Integrated Microbial Genomes Database Build conceptual understanding of: o Evolutionary relationships among genomes o Genome organization o Power and limitations of bioinformatics o Protein structure and function o Transcriptional and translational signals Develop basic scientific research skills such as: o Reading and evaluating primary literature o Developing hypotheses and interpreting data o Drawing conclusions from a collection of evidence o Working collaboratively o Working with real data

17. IMG-ACT M ODULAR A NNOTATION 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

18. ANNOTATION Module TitleDescription Mod 1: Basic InformationDNA 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

19. M ODULE C ONCEPTS Basic Information

20. 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 Acknowledgements