Difference between revisions of "PWY-5885"
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(Created page with "== sjapGEM description == ''Saccharina japonica'' is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than U...") |
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| − | == | + | == SJAPGEM description == |
''Saccharina japonica'' is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value ([http://www.fao.org/fishery/culturedspecies/Laminaria_japonica/en#tcNA008C Chen J., FAO website, accessed on january 10th, 2019]). | ''Saccharina japonica'' is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value ([http://www.fao.org/fishery/culturedspecies/Laminaria_japonica/en#tcNA008C Chen J., FAO website, accessed on january 10th, 2019]). | ||
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | ||
| − | The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:model.xml|Model]] containing | + | The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources: |
* Based on annotation data: | * Based on annotation data: | ||
** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | ||
| − | *** Creation of a metabolic network containing | + | *** Creation of a metabolic network containing 2552 reactions |
* Based on orthology data: | * Based on orthology data: | ||
** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ||
| − | *** From template ''NANNOCHLOROPSIS_SALINA'' ([https://doi.org/10.1186/s12918-017-0441-1 Loira et al., 2017]) creation of a metabolic network containing: | + | *** From template ''NANNOCHLOROPSIS_SALINA'' ([https://doi.org/10.1186/s12918-017-0441-1 Loira et al., 2017]) creation of a metabolic network containing: 589 reactions |
| − | *** From template ''ARABIDOPSIS_THALIANA'' ([https://doi.org/10.1104/pp.109.148817 De Oliveira dal'Molin et al., 2010]) creation of a metabolic network containing: | + | *** From template ''ARABIDOPSIS_THALIANA'' ([https://doi.org/10.1104/pp.109.148817 De Oliveira dal'Molin et al., 2010]) creation of a metabolic network containing: 419 reactions |
| − | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: | + | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1492 reactions |
* Based on expertise: | * Based on expertise: | ||
| − | *** | + | *** 64 reaction(s) added |
* Based on gap-filling: | * Based on gap-filling: | ||
** Tool: [https://pypi.python.org/pypi/meneco meneco] | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | ||
| − | *** | + | *** 106 reaction(s) added |
== Collaborative curation == | == Collaborative curation == | ||
Revision as of 13:07, 27 August 2019
SJAPGEM description
Saccharina japonica is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value (Chen J., FAO website, accessed on january 10th, 2019). Its draft genome sequence was published in 2015 (Ye et al., Nature Communications). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast (Dittami and Corre, 2017). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945).
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of Saccharina japonica results to a Genome scale Model containing 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Tool: Pathway tools
- Creation of a metabolic network containing 2552 reactions
- Tool: Pathway tools
- Based on orthology data:
- Tool: Pantograph
- From template NANNOCHLOROPSIS_SALINA (Loira et al., 2017) creation of a metabolic network containing: 589 reactions
- From template ARABIDOPSIS_THALIANA (De Oliveira dal'Molin et al., 2010) creation of a metabolic network containing: 419 reactions
- From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1492 reactions
- Tool: Pantograph
- Based on expertise:
- 64 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 106 reaction(s) added
- Tool: meneco
