Difference between revisions of "Main Page"
Jump to navigation
Jump to search
(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...") |
(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...") |
||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 5: | Line 5: | ||
Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | ||
| − | The automatic reconstruction of ''Fibrobacter | + | The automatic reconstruction of ''Fibrobacter succinogene S85'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1565 reactions, 1586 metabolites, 1317 genes and 931 pathways. This GeM was obtained based on the following sources: |
* Based on annotation data: | * Based on annotation data: | ||
| − | ** Creation of a metabolic network containing | + | ** Creation of a metabolic network containing 827 reactions |
* Based on orthology data: | * Based on orthology data: | ||
** Creation of a global metabolic network containing 377 reactions | ** Creation of a global metabolic network containing 377 reactions | ||
* Based on expertise: | * Based on expertise: | ||
| − | ** | + | ** 490 reaction(s) added |
* Based on gap-filling: | * Based on gap-filling: | ||
| − | *** | + | *** 75 reaction(s) added |
*List of tools used: | *List of tools used: | ||
** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools] | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools] | ||
** Tool: [https://github.com/davidemms/OrthoFinder Orthofinder] | ** Tool: [https://github.com/davidemms/OrthoFinder Orthofinder] | ||
| + | |||
** Tool: [https://pypi.python.org/pypi/meneco Meneco] | ** Tool: [https://pypi.python.org/pypi/meneco Meneco] | ||
| − | |||
[[FILE:venn.png|frameless|border]] | [[FILE:venn.png|frameless|border]] | ||
Latest revision as of 11:09, 17 October 2022
description
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of Fibrobacter succinogene S85 results to a Genome scale Model containing 1565 reactions, 1586 metabolites, 1317 genes and 931 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Creation of a metabolic network containing 827 reactions
- Based on orthology data:
- Creation of a global metabolic network containing 377 reactions
- Based on expertise:
- 490 reaction(s) added
- Based on gap-filling:
- 75 reaction(s) added
- List of tools used:
- Tool: PathwayTools
- Tool: Orthofinder
- Tool: Meneco
