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Other Pathway/Genome Databases
Curated Pathway/Genome Databases for many organisms have been created using our Pathway Tools software by a variety of institutions and are available from the following Web sites.
In addition to accessing them through the Web, many of these PGDBs can be downloaded to your local copy of Pathway Tools through the PGDB Registry described later in this page.
| Database | Scope | Organization |
| AcypiCyc |
Acyrthosiphon pisum Aphis glycines Daktulosphaira vitifoliae Diuraphis noxia Myzus cerasi Myzus persicase Rhoplalossiphum padi |
Universite de Lyon |
| ArthropodaCyc | PGDBs for 32 arthropods | ArthropodaCyc group, France |
| CacaoCyc | Theobroma Cacao | MARS, USDA-ARS, IBM,NCGR, Clemson U., HudsonAlpha Institute, Indiana U., Washington State U. |
| CalbiCyc | Candida albicans | Department of Genetics, Stanford U., USA |
| Cathacyc | Catharanthus roseus | European Union Seventh Framework Programme, European Molecular Biology Organization and the European Commission support. |
| CottonCyc |
Gossypium raimondii Gossypium hirsutum Gossypium arboreum Gossypium barbadense Gossypium turneri |
CottonGen, Washington State University |
| DiatomCyc | Phaeodactylum tricornutum | Center for Plant Systems Biology, University of Ghent, Belgium |
| Gramene |
Brachypodium distachyon Oryza sativa Nipponbare (Japonica rice) Sorghum bicolor BTX623 Zea mays and mirrored PGDBs for 9 organisms |
Gramene curators (CSHL, OSU, EMBL-EBI) |
| GutCyc | 418 gut bacteria available as flat files only | University of British Columbia, Stanford University |
| MicroScope | PGDBs for 3749 Organisms | C. Medigue, Genoscope, France |
| Nannocyc | PGDBs for 3 Nannochloropsis species | Single Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology |
| PlantCyc | PGDBs for 101 plants | Plant Metabolic Network, Carnegie Institution, USA |
| PseudoCyc | Pseudomonas aeruginosa | F. Brinkman, Pseudomonas Genome Project, Simon Fraser U., Canada |
| SoyCyc | Glycine max | SoyBase |
| Trypanocyc |
Trypanosoma brucei Leishmania major |
INRA Toulouse, France |
| USDA Bacterial Genomes | Mannheimia haemolytica Strain USDA-ARS-USMARC-183 Salmonella enterica Strain serovar Montevideo str. CDC 2012K-1544 |
USDA SciNet |
| VitisCyc and others |
Vitis vinifera Eucalyptus grandis Fragaria vesca and mirrored PGDBs for 10 organisms |
Center for Genome Research and Biocomputing, Oregon State University |
| Yeast Biochemical Pathways | Saccharomyces cerevisiae | SGD Curators, Stanford U., USA |
Contact us if you'd like your PGDB added to this list. |
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Registry of Downloadable Pathway/Genome Databases
The PGDB Registry allows users who have installed Pathway Tools locally to easily download PGDBs created by others, or share PGDBs that they have created. Advantages of this approach are that it makes the full power of Pathway Tools available for other PGDBs, and it allows comparative analysis of multiple PGDBs within the same instance of Pathway Tools. [access registry]
Create Your Own Pathway/Genome Database
Interested in creating a pathway/genome DB for your genome? [learn more]
