Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

Rabie Saidi, Imene Boudellioua, Maria J. Martin, Victor Solovyev

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.
Original languageEnglish (US)
Title of host publicationBiological Networks and Pathway Analysis
PublisherSpringer Nature
Pages311-331
Number of pages21
ISBN (Print)9781493970254
DOIs
StatePublished - Aug 29 2017

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

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