Cbcb:Pop-Lab:Chris-Report: Difference between revisions
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**Waterflea, ''Daphnia pulex'' | **Waterflea, ''Daphnia pulex'' | ||
*Incomplete genomes that require blast | *Incomplete genomes that require blast | ||
**Gastropod Snail, Lottia gigantea | **Gastropod Snail, ''Lottia gigantea'' | ||
**Polychaete Worm, Capitella sp | **Polychaete Worm, ''Capitella sp'' | ||
*Future genomes | *Future genomes | ||
**Leech, ''Helobdella robusta'' | **Leech, ''Helobdella robusta'' | ||
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**Sea Slug,'' Aplysia californica'' | **Sea Slug,'' Aplysia californica'' | ||
**Snail,'' Biomphalaria glabrata'' | **Snail,'' Biomphalaria glabrata'' | ||
**Slime-mold, Dictyostelium purpureum QSDP1 | **Slime-mold, ''Dictyostelium purpureum QSDP1'' | ||
*Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes. | *Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes. | ||
Revision as of 02:23, 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.