The University of Minnesota Pathway Prediction System: Multi-level prediction and visualization

Junfeng Gao, Lynda B.M. Ellis, Lawrence P. Wackett

Research output: Contribution to journalArticlepeer-review

47 Scopus citations

Abstract

The University of Minnesota Pathway Prediction System (UM-PPS, http://umbbd.msi.umn.edu/predict/) is a rule-based system that predicts microbial catabolism of organic compounds. Currently, its knowledge base contains 250 biotransformation rules and five types of metabolic logic entities. The original UM-PPS predicted up to two prediction levels at a time. Users had to choose a predicted product to continue the prediction. This approach provided a limited view of prediction results and heavily relied on manual intervention. The new UM-PPS produces a multi-level prediction within an acceptable time frame, and allows users to view prediction alternatives much more easily as a directed acyclic graph.

Original languageEnglish (US)
Pages (from-to)W406-W411
JournalNucleic acids research
Volume39
Issue numberSUPPL. 2
DOIs
StatePublished - Jul 1 2011

Bibliographical note

Funding Information:
U.S. National Science Foundation (NSF0543416 to L.E. and L.W.); Minnesota Supercomputing Institute. Funding for open access charge: University of Minnesota.

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