PoplarCyc 3.0



PoplarCyc, a genus-level database was developed largely computationally using:

  1. A newly developed enzyme annotation pipeline from the PMN
  2. The Populus trichocarpa 1.1 genome release provided by JGI
  3. The Pathologic pathway prediction software from SRI International


  • The majority of the pathways found in PoplarCyc are based on computational predictions, however, these pathways have been reviewed by curators. Comments and references have often been added to try to explain the specific criteria used to establish their potential validity.
  • A few manually curated pathways have been added if there is experimental support for their existence in Populus species or hybrids. The associated enzymes have been included in the database even if they were not isolated from or studied in Populus trichocarpa. In these cases, comments were added on the enzyme page to indicate the species or hybrid of origin (see isoprene synthase). When no species is indicated in the enzyme comments, the enzyme sequence has been taken from Populus trichocarpa.
  • As in the case for all PMN databases, evidence codes on both the pathway and enzyme pages can be used to determine the experimental or computational support for the information in PoplarCyc.