Difference between revisions of "PWY-3861"
Jump to navigation
Jump to search
| Line 1: | Line 1: | ||
| − | + | == 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]). | |
| + | Its draft genome sequence was published in 2015 ([http://doi.org/10.1038/ncomms7986 Ye et al., Nature Communications]). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast ([https://doi.org/10.7717/peerj.4073 Dittami and Corre, 2017]). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on the abscisic acid synthesis pathway (PWY-695). | ||
| − | == | + | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == |
| − | + | Model summary: [[MEDIA:summary.txt|summary]] | |
| − | * [ | + | |
| − | * [https:// | + | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] |
| − | * [https:// | + | |
| − | * [https:// | + | The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources: |
| + | * Based on annotation data: | ||
| + | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | ||
| + | *** Creation of a metabolic network containing 2568 reactions | ||
| + | * Based on orthology data: | ||
| + | ** 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: 1337 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: 901 reactions | ||
| + | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1498 reactions | ||
| + | * Based on expertise: | ||
| + | *** 17 reaction(s) added | ||
| + | * Based on gap-filling: | ||
| + | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | ||
| + | *** 91 reaction(s) added | ||
| + | |||
| + | == 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: gabriel.markov@sb-roscoff.fr | ||
Revision as of 10:04, 26 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 the abscisic acid synthesis pathway (PWY-695).
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 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Tool: Pathway tools
- Creation of a metabolic network containing 2568 reactions
- Tool: Pathway tools
- Based on orthology data:
- Tool: Pantograph
- From template NANNOCHLOROPSIS_SALINA (Loira et al., 2017) creation of a metabolic network containing: 1337 reactions
- From template ARABIDOPSIS_THALIANA (De Oliveira dal'Molin et al., 2010) creation of a metabolic network containing: 901 reactions
- From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1498 reactions
- Tool: Pantograph
- Based on expertise:
- 17 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 91 reaction(s) added
- Tool: meneco
