PMN Release 3.0

October 2009


Overall Highlights: 

New database:
Using a newly developed PMN enzyme annotation pipeline, the Populus trichocarpa 1.1 genome release sequences provided by JGI, and the Pathologic software from SRI International, the PMN has created the PoplarCyc 1.0 database. Now, researchers focusing on this important tree can see predicted enzymes mapped onto metabolic pathways and can overlay their microarray and metabolomic experimental results onto a poplar metabolic map using the OMICs viewer.

New tool:
Researchers can now do BLAST analyses using nucleotide or protein sequences at the PMN. Two BLAST datasets are available:

  • “Reference Enzymes” (14,187 proteins) includes enzymes taken from a number of different data repositories that have experimentally supported* enzyme activity and known protein sequences. Both plant and non-plant enzymes are contained in this data set.
  • “PlantCyc Enzymes” (6411 proteins) includes the enzymes found in the PlantCyc database that have known protein sequences. Both experimentally and computationally supported enzymes are present in this data set.

New data:

  • Many new pathways, enzymes, reactions, and compounds have been added to the suite of PMN databases.
  • The new PMN enzyme annotation pipeline was also applied to the Arabidopsis thaliana genome, resulting in many changes to the set of computationally predicted annotations found in AraCyc.
Collaborator Release Notes: 

You can find more information on the releases provided by our collaborators at MetaCyc, the multi-species, multi-kingdom database, in their Release Notes.