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    Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

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    Type
    Book Chapter
    Authors
    Saidi, Rabie
    Boudellioua, Imene cc
    Martin, Maria J.
    Solovyev, Victor cc
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2017-08-29
    Online Publication Date
    2017-08-29
    Print Publication Date
    2017
    Permanent link to this record
    http://hdl.handle.net/10754/625999
    
    Metadata
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    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.
    Citation
    Saidi R, Boudellioua I, Martin MJ, Solovyev V (2017) Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways. Biological Networks and Pathway Analysis: 311–331. Available: http://dx.doi.org/10.1007/978-1-4939-7027-8_12.
    Sponsors
    The second author conducted this work as part of a research internship at the European Bioinformatics Institute, UniProt team. The funding for this internship was provided by King Abdullah University of Science and Technology. The authors would also like to thank UniProt Consortium for their valuable support and feedback on the development of this work.
    Publisher
    Springer Nature
    Journal
    Biological Networks and Pathway Analysis
    DOI
    10.1007/978-1-4939-7027-8_12
    Additional Links
    https://link.springer.com/protocol/10.1007%2F978-1-4939-7027-8_12
    ae974a485f413a2113503eed53cd6c53
    10.1007/978-1-4939-7027-8_12
    Scopus Count
    Collections
    Computer Science Program; Computational Bioscience Research Center (CBRC); Book Chapters; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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