Microbial Genomics Workshop
| Online Tools |
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| Artemis BLAST ClustalX COGs EBI Enzyme GOLD IMG InterPro KEGG NCBI/GenBank Pfam PIR Sequencher SwissPROT VISTA |
Monday, April 24, 4:30-8:00 pm
| 4:30-5:00 | 1. Introduction Karen Kelly, David Gilbert, and Nikos Kyrpides Slides Welcome and overview of the workshop. |
|---|---|
| 5:00-5:30 | 2. Why Study Microbes? Hector Garcia Martin Why the work done with microbes is so important. Slides |
| 5:30-6:00 | 3. JGI Sequencing Process Damon Tighe Flash animation showing how JGI determines the genomic sequence of an organism. 30-minute Flash animation How Sequencing is Done |
| 6:00-6:45 | 4. Microbial Genome Assembly and Finishing Alla Lapidus Automatically assembled genomes are never correct. The problems are solved in finishing. Slides Sequencher PC | Sequencher Mac Chromatograms |
| 6:45-7:15 | Dinner |
| 7:15-8:00 | 5. The Quest for Genes Natalia Ivanova What is a gene, and how do we find the coding regions? Slides Artemis (installs for PC, Mac, Unix) ferroplasma.gbk ferroplasma-DNA.gbk |
Tuesday, April 25, 4:30-8:00 pm
| 4:30-5:00 | 6. Data Sources Kostas Mavrommatis After the sequence is assembled, where does it go? What kind of sequence data is available to the public? Slides | Handout NCBI/GenBank EBI SwissPROT PIR Pfam COGs InterPro Enzyme KEGG GOLD |
|---|---|
| 5:00-5:30 | 7. Annotation: Gene/Protein Relationships Thanos Lykidis After a gene has been located, how is it characterized? How do we discover the role of an enzyme in a metabolic pathway? Slides |
| 5:30-6:00 | 8. Experiences as a JGI Intern Igor Bogorad, student intern Igor, our student intern, will show participants how he does qualitative analysis. This section will give participants a feel for the kind of work required during an internship at DOE JGI. Slides: long version | short version DOE JGI's Integrated Microbial Genomes (IMG) Artemis BLAST VISTA Tools |
| 6:00-6:30 | Dinner |
| 6:30-7:30 | 9. Phylogenomics Pilar Francino and Falk Warnecke Fusing genomics and evolution enables us to develop phylogenetic trees based on sequence data. FW Slides PF Slides IMG ClustalX for PC or Unix Sequences |
| 7:30-8:00 | 10. Metagenomics Phil Hugenholtz Using high-throughput sequencing directly on environmental samples. |
Speaker Biographies (Word file)
