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For example, I want to use the agaricales_odb10 as reference database to pick single copy orthologs, how can I change the Fungi_odb10 to Agaricales_odb10?
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The UI may be fiddly, but we should at least allow people to do things like this via the command line. It shouldn't be hard using e.g. scigraph-python
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* **PTHR ID & PTN node:**
PTN000385050 (PTHR15004)
* **Sequences with problematic annotation (ID + gene/protein name):**
Fly GatC (FBgn0064115)
Fly GatA (FBgn0260779)
Fly GatB (FBgn0039153)
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sjm41 updated
4 months ago
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Depends on #3
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Promoter pBetI exists in both TetR Orthologs and the Small Mol packages, but with different sequences I believe. I haven't taken a closer look at this, but just wanted to flag it.
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Path:
`/api/expressions/{bel}/orthologs`
`{bel}` term example:
- `p(HGNC:AKT1)`
`{bel}` statement example:
- `p(HGNC:AKT1) => bp(GOBP:"apoptotic process")`
extra parameters
- `{namespace_preferenc…
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- [x] Cookies
- [ ] Manager
- [ ] DatabaseManagement
- [x] ProjectManagement
- [ ] Orthologs
- [ ] Align
- [x] Blast
- [ ] Genbank
- [x] CompGenetics
- [ ] Phylogenetics
- …
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http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000251
broaden this pathway to "acyl-CoA metabolic process"
https://www.pombase.org/results/fr…
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Hi,
I was wondering if the SHOOT website has an API or some way to submit proteins via command line? I have a few hundreds genes I'd like to run through SHOOT to identify orthologs.
Thanks
Jon
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http://monarchinitiative.org/gene/NCBIGene:5077
http://monarchinitiative.org/gene/NCBIGene:5077
Not only are there models via phenotype similarity on Phenogrid, but there are also orthologs of PAX3 i…