B. infantis pathway/genome database

Pathway tools overview


Pathway Tools is a software package which provides powerful visualization solutions for systems biology. Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.


One uses Pathway Tools to develop an organism-specific pathway/genome database (PGDB). In this instance a PGDB was created for B. infantis ATCC15697 (Binfcyc).

Some features of Pathway Tools include:

  • Display and browse metabolic pathways integrated into networks.
  • A genome browser which displays predicted operons.
  • Where experimental data exists, one could integrate expression data to develop a regulon-level understanding of the organism.
  • Similarly, other visual analyses of omics data can be overlayed onto metabolic or regulatory networks or the whole genome.
  • Also, additional PGDBs can be downloaded for comparative genomic purposes


For more information, please visit the Pathway Tools website.



B. infantis PGDB

To obtain Pathway Tools to examine the B. infantis PGDB on a local computer please visit here and follow software installation instructions found here.
It is highly advisable to consult the included documentation prior to uploading the generated PGDB. For more advanced users who wish to proceed to PGDB import, ptools has a webpage that discusses importing a flat file: Import
Additional notes on the B. infantis PGDB:
The database was created with genbank accession CP001095.1 using PathoLogic v. 13.0. The database was constructed with an automated build following trial parsing to check for naming consistency. The PGDB was further refined by assigning probable enzymes, creating likely protein complexes, predicting operon structure, inferring transport function, and using BLAST to fill holes in the predicted pathways. Pathways were rescored following each step and the consistency checker was invoked prior to generating the flat file.