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.

Target audience:
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) –