Cbcb:Pop-Lab:Chris-Report: Difference between revisions
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== Mar 2, 2009 == | == Mar 2, 2009 == | ||
===Tasks=== | |||
'''Intergenic space and gene ontology work with Cristian''' | '''Intergenic space and gene ontology work with Cristian''' | ||
*Approach | *Approach | ||
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*Update elements based on Adam's changes to Insignia. | *Update elements based on Adam's changes to Insignia. | ||
*Find something to write about. | *Find something to write about. | ||
http://med.stanford.edu/news_releases/2008/july/aging-worm.html | |||
Revision as of 02:25, 2 March 2009
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.
http://med.stanford.edu/news_releases/2008/july/aging-worm.html