Cbcb:Pop-Lab:Chris-Report: Difference between revisions
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== 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'' | |||
Revision as of 02:10, 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