Toward the automated generation of genome-scale metabolic networks in the SEED

doi:10.1186/1471-2105-8-139

BMC Bioinformatics

Volume 8

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DeJongh M
Formsma K
Boillot P
Gould J
Rycenga M
Best A

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Boillot P
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Rycenga M
Best A
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Research article

Toward the automated generation of genome-scale metabolic networks in the SEED

Matthew DeJongh¹ , Kevin Formsma¹^,2 , Paul Boillot¹ , John Gould¹ , Matthew Rycenga³^,4 and Aaron Best²

¹Department of Computer Science, Hope College, 27 Graves Place, Holland, MI, USA

²Department of Biology, Hope College, 35 E. 12^thSt., Holland, MI, USA

³Department of Chemistry, Hope College, 35 E. 12^thSt., Holland, MI, USA

⁴Department of Chemistry, University of Washington, Box # 351700, Seattle, WA, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:139doi:10.1186/1471-2105-8-139


Published:	26 April 2007

Additional files

Additional File 1:

Reverse-engineering reactions from E. coli, H. pylori, and L. lactis models after S. aureus network curation. The table shows the distribution of reactions in relation to subsystems and functional roles in the SEED subsequent to S. aureus curation.

Format: PDF Size: 78KB Download file

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Additional File 2:

Subsystems and scenarios used in reaction network generation. The table lists the subsystem names, subsystem abbreviations, and scenario names that were curated in preparation for reaction network generation; subsystems are grouped according to metabolic categories. An "x" indicates those subsystems and scenarios used in the generation of the S. aureus iSB619 reaction network. Subsystems and scenarios identified as complete for generation of E. coli, H. pylori and L. lactis networks are also indicated.

Format: PDF Size: 59KB Download file

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Additional File 3:

Reverse-engineering reactions from H. pylori and L. lactis models after S. aureus and E. coli network curation. The table shows the distribution of reactions in relation to subsystems and functional roles in the SEED subsequent to S. aureus and E. coli curation.

Format: PDF Size: 79KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 4:

Distribution of reverse-engineered reactions from S. aureus iSB619 model. The table shows the distribution of reactions in relation to subsystems and functional roles in the SEED for the S. aureus model.

Format: PDF Size: 66KB Download file

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Additional File 5:

Correspondences among iSB619 model and KEGG compound and reaction identifiers. The tables provide correspondences among iSB619 model compound and reaction identifiers and KEGG compound and reaction identifiers. Model reactions without matches to KEGG reactions or with inexact matches to KEGG reactions used in the generation of the S. aureus model are indicated by "add as is" and "...is similar", respectively. Conversion reactions are also listed.

Format: XLS Size: 82KB Download file

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