Comparative genomics workshop

May 28-29, 2015

Prof. Thérésa Bridget Fitzpatrick

Prof. Dr. Andrew Hanson (Horticultural Sciences Department, University of Florida, USA)
Postdoc Dr. Tom Niehaus (Horticultural Sciences Department, University of Florida, USA)

A two-day workshop on comparative genomics, comprising formal lectures as well as hands-on instruction. The workshop content is of interest to microbiologists, plant scientists, and biomedical scientists. WORKSHOP AIMS - Grasp the basic concepts and challenges in COMPARATIVE GENOMICS (types of association evidence, the subsystem approach to gene annotation, the ‘orphan gene’ and ‘orphan enzyme’ problems). - Understand how prokaryote and eukaryote comparative genomics can be used synergistically to PREDICT GENE FUNCTION. - Be familiar with the capabilities of the STRING and SEED databases and their comparative genomics tools. - Be equipped for basic use of the SEED and related platforms to annotate genes, to create and curate subsystems for metabolic pathways, and to use subsystems to predict functions for genes. - Be able to use advanced SEED functions that increase the efficiency of GENE ANNOTATION and allow the user to focus on particular genes and genomes.

UniGe, room 0019 Sciences III

Map

LOGISTICS

- The most suitable venue is a computer lab with all computers the same and running the Firefox browser. Using individual laptops is not impossible but creates problems for troubleshooting due to different operating systems, software versions, and languages.

- The workshop takes two full days (9 am to 5 pm) with a 1 hour break for lunch. It will combine 30% formal instruction and 70% individual hands-on tuition. Participants should plan to attend for the whole two days. Lectures and instruction are interspersed in a balanced mix as follows:

Day 1

Classroom sessions:

-Outline of phylogenomics approaches, giving selected case-histories. 

-Brief review of public on-line resources (SEED, STRING).

 Hands-on computer sessions:

-Use of STRING to recapitulate historic gene discoveries made via clustering and co-distribution.

-Introduction of the SEED database – its genomes, how to navigate, clustering tools, essentiality data.

-Defining a subsystem in SEED for each participant.

Day 2

Classroom sessions:

-User rules for the SEED annotator. Appropiate syntax used for annotations. Techniques used for copying and building a subsystem. Description of the subsystem spreadsheet tools. Use of SEED annotation tools with selected target genes that participants will annotate themselves in the hands on session.  

Hands-on computer sessions:

-Creation and curation of a SEED subsystem incorporating novel genes for each participant.

PARTICIPANT REQUIREMENTS

To benefit from the course, participants need:

- To have some familiarity with the basics of GenBank entries, Blast searches, sequence alignment and phylogenetic analysis, prediction programs for organellar targeting etc, and microarray databases.

- To know elementary microbiology (e.g. that bacteria and archaea are different, that prokaryotic lifestyles and metabolic capacities differ enormously, and what operons are).

- To be acquainted with KEGG pathways is helpful.

- To maximize the relevance of the hands-on instruction, and participant motivation, participants are encouraged to propose problems from their own research programs. These will be checked beforehand by instructors to ensure their suitability. These problems could be, for example, (1) a plant gene of unknown function that has good homologs in prokaryotes, or (2) an enzyme that is known to exist but for which a gene has not yet been found.

During the workshop, the instructors will help the participants to apply the genomics techniques to their research problem In case (1) above, we can try to predict a function for the gene; in case (2) we can try to find the gene corresponding to the enzyme.

Participants who do not have their own suitable problem can be assigned one.

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