The PMN has several tools available for analyzing the data presented in PlantCyc and the other species-specific metabolic databases.
PMN BLAST allows users to perform sequence similarity searches using many unique enzyme sets provided by the PMN such as:
- “Reference Enzymes (2.0)” includes trusted enzymes taken from SwissProt 15.3 (2011) that have known protein sequences. Both plant and non-plant enzymes are contained in this data set.
- “PlantCyc Enzymes” includes all the enzymes found in the PlantCyc database that have known protein sequences. Both experimentally and computationally supported enzymes are present in this data set.
Tutorials provide background information and step-by-step instructions for using some of the tools available at the PMN website.
We also provide links to useful external resources for members of the PMN community.
PMN Tools (provided by SRI International)
Many tools essential for the PMN databases have been created by and are maintained by the Bioinformatics Research Group of Dr. Peter Karp at SRI International
- Pathway Tools software is used to enter, house, display, and analyze the metabolic pathway data present in PMN databases. The Query Page and other tools listed below are elements of the Pathway Tools program.
- The PathoLogic component of Pathway Tools is used to predict metabolic pathways from annotated genes in order to create new databases and refine existing databases.
The PMN is grateful for the tireless support provided by members of the technical team at SRI.
This page allows users to search for pathways, reactions, enzymes, and compounds in the PlantCyc multi-species database, or in any of the species-specific metabolic pathway databases such as AraCyc.
Users can also browse through or obtains lists of pathways and compounds and get summary information for specific organisms at this Query Page.
Advanced Query Page – (Tutorial)
This page allows users to perform more high-powered and selective searches through PlantCyc and the other species-specific databases
Metabolic (Cellular) Overview / Omics Viewer –(Tutorial) (Sample data files)
Each Metabolic (Cellular) Overview provides the user with a ‘bird’s eye’ view of the metabolic pathways that are entered in each species-specific database. For example, PoplarCyc has a metabolic map that shows a large image of all of the pathways entered from poplar. Users can zoom in and out, click on specific compounds or pathways to get more detailed information. or search for and highlight specific compounds, pathways, enzymes, and more. Currently, no metabolic overview is available for the PlantCyc database.
(Note: These pages may take a moment to load).
Old Omics Viewer – (Tutorial) [AraCyc Omics Viewer]
Please note: The functions performed by the Old Omics Viewer can now be performed by the Metabolic (Cellular) Overview / Omics Viewer. This version of the Old Omics Viewer will no longer be supported in future releases of the PMN.
Tbe Omics Viewer is a powerful tool that can be used to overlay transciptional, proteomic, and metabolomic data on species-specific metabolic map. This program allows all the changes in a plant’s metabolism caused by a mutation, a specific stress condition, etc., to be visualized in a global context. This feature is not currently available for multiorganism databases, such as PlantCyc.
Stand-alone version of Pathway Tools Software and Data
- Pathway Tools software is responsible for creating and displaying PlantCyc and the other species-specific databases such as LycoCyc, MedicCyc, etc.
- The BioCyc database set includes species-specific databases from many kingdoms, as well as MetaCyc, a kindgom-spanning multi-organism metabolic pathway database.
- You can use this software and data package to create your own species-specific metabolic database and to perform more powerful analyses using existing data.
- To download, use this license form and select the appropriate “Organization Type” at the bottom of the page
PMN Tools (provided by SGN (Solanaceae Genomics Network))
PerlCyc perlcyc.pm is a Perl module for accessing internal Pathway Tools functions.
JavaCyc javacyc is a java class for accessing internal Pathway Tools functions.
Please check our “Useful Sites” drop-down menu from the menu bar for even more links, and please send us suggestions for any additional links that would be helpful to the PMN community.