Difference between revisions of "CPD-4702"
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(Created page with "== ESUBGEM description == ''Ectocarpus subulatus'' is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 ([https://doi.o...") |
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| − | + | == ESUBGEM description == | |
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| − | + | ''Ectocarpus subulatus'' is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 ([https://doi.org/10.1016/j.margen.2020.100740 Dittami et al., Marine Genomics]), alongside with a first version of a genome-scale metabolic network (still available at http://gem-aureme.irisa.fr/sububftgem). In a follow-up study (Girard et al., ''in preparation'') we are now curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238). | |
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| − | | | + | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == |
| − | + | Model summary: [[MEDIA:summary.txt|summary]] | |
| − | | | + | |
| − | + | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | |
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| + | The automatic reconstruction of ''Ectocarpus subulatus strain BFT'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 2086 reactions, 2204 metabolites, 5052 genes and 1152 pathways. This GeM was obtained based on the following sources: | ||
| + | * Based on annotation data: | ||
| + | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools] | ||
| + | ** Creation of a metabolic network containing 1459 reactions | ||
| + | * Based on expertise: | ||
| + | ** 480 reaction(s) added | ||
| + | * Based on orthology data: | ||
| + | ** Creation of a global metabolic network containing 417 reactions | ||
| + | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ||
| + | *** From template ''a.taliana.aragem'' creation of a metabolic network containing: 417 reactions | ||
| + | |||
| + | [[FILE:venn.png|frameless|border]] | ||
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| + | == Collaborative curation == | ||
| + | * Suggest reactions to add or remove: | ||
| + | ** Download this [[MEDIA:Add_delete_reaction.csv|form]] | ||
| + | * Suggest new reactions to create and add: | ||
| + | ** Download this [[MEDIA:Reaction_creator.csv|form]] | ||
| + | * '''Follow the examples given in the form(s) to correctly share your suggestions''' | ||
| + | * Send the filled form(s) to: gem-aureme[AT]inria.fr | ||
Revision as of 17:58, 13 January 2021
ESUBGEM description
Ectocarpus subulatus is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 (Dittami et al., Marine Genomics), alongside with a first version of a genome-scale metabolic network (still available at http://gem-aureme.irisa.fr/sububftgem). In a follow-up study (Girard et al., in preparation) we are now curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of Ectocarpus subulatus strain BFT results to a Genome scale Model containing 2086 reactions, 2204 metabolites, 5052 genes and 1152 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Tool: PathwayTools
- Creation of a metabolic network containing 1459 reactions
- Based on expertise:
- 480 reaction(s) added
- Based on orthology data:
- Creation of a global metabolic network containing 417 reactions
- Tool: Pantograph
- From template a.taliana.aragem creation of a metabolic network containing: 417 reactions
