Comparative Genomics using SEED – training workshop
Comparative Genomics using SEED
15-16 July 2010
University of Nottingham – Sutton Bonington Campus
A two day, hands-on workshop addressing the challenge of finding functions for the many genes of unknown function that occur in all sequenced genomes.
To teach people how to use public comparative genomics databases – particularly a very powerful one called SEED – to predict functions for genes common to plants (or other eukaryotes) and prokaryotes.
Academic staff, postdocs and research students, especially those working in plant, animal, and microbial metabolism.
- some familiarity with the basics of GenBank entries, Blast searches, sequence alignment and phylogenetic analysis, prediction programs for targeting etc, and microarray databases
- elementary microbiology (e.g. that bacteria and archaea are different, that prokaryotic lifestyles and metabolic capacities differ enormously, and what operons are).
- Some acquaintance with KEGG pathways is helpful
- ideally participants “bring their own gene” of interest
- The best situation is for PIs to attend with their lab members
Andrew Hanson (University of Florida)
Day 1 classroom sessions
- Outline phylogenomics approaches, giving selected case-histories
- Briefly review public on-line resources (SEED, STRING)
Day 1 hands-on computer sessions
- Use STRING to recapitulate historic gene discoveries made via clustering and co-distribution
- Introduce the SEED database – its genomes, how to navigate, clustering tools, essentiality data
- Teach SEED annotation tools using selected target genes that participants annotate themselves
Day 2 hands-on computer sessions
- Creation and curation of a SEED subsystem incorporating the above novel genes
- Using the subsystem to develop hypotheses about novel genes’ function
More information is available from the course webpages
Places are limited to 12 – food and refreshments will be provided.
Places will be allocated on a “first come, first served” basis, subject to meeting course requirements.
If you are interested in attending, please contact [person name=’Susie Lydon’/] (CPIB Outreach Officer) – firstname.lastname@example.org