Cbcb:Pop-Lab:Chris-Report

Mar 2, 2009

Tasks

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
  • Slime-mold, Dictyostelium purpureum QSDP1
• Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.

Partitioning System

• Splitting contigs based on "subgroup" information - essentially extending breaking up an entire assembly into multiple "sub-assemblies" each containing just reads from a single subgroup.

Conserved genomic elements in bacteria

• Update elements based on Adam's changes to Insignia.
• Find something to write about.

Interesting Stuff

• New insights into aging based on transcription factors, Prevailing theory of aging challenged in Stanford worm study