Cbcb:Pop-Lab:Chris-Report: Difference between revisions

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== Mar 2, 2009 ==
== Mar 2, 2009 ==
'''Intergenic Space and Gene Ontology work with Cristian'''   
'''Intergenic space and gene ontology work with Cristian'''   
*Approach
*Approach
   *Get the gene-spacing information - typically a simple parse of GFF files, if they are available.
   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.
   Get the gene function information - use GO if available.
   *Rank the genes based on 5' spacing size.
   Rank the genes based on 5' spacing size.
   *Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge
   Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge
*Completed genomes
*Completed genomes
**Anenome, ''Nematostella vectensis''
**Anenome, ''Nematostella vectensis''
Line 18: Line 18:
**Sea Slug,'' Aplysia californica''
**Sea Slug,'' Aplysia californica''
**Snail,'' Biomphalaria glabrata''
**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.

Revision as of 02:22, 2 March 2009

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
    • 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.
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