Cbcb:Pop-Lab:Chris-Report

Mar 2, 2009

Intergenic Space and Gene Ontology work with Cristian

• Approach

 *Get the gene-spacing information - typically a simple parse of GFF files, if they are available.
 *Get the gene function information - use GO if available.
 *Rank the genes based on 5' spacing size.
 *Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge

• Completed genomes
  • Anenome, Nematostella vectensis
  • Frog, Xenopus tropicalis
  • Waterflea, Daphnia pulex
• Incomplete genomes that require blast
  • Gastropod Snail, Lottia gigantea
  • Polychaete Worm, Capitella sp
• Future genomes
  • Leech, Helobdella robusta
  • Flatworm (Planaria), Schmidtea mediterranea
  • Sea Slug, Aplysia californica
  • Snail, Biomphalaria glabrata