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Applying Logic Programming to Derive Novel Functional Information of Genomes

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Practical Aspects of Declarative Languages (PADL 1999)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1551))

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Abstract

This paper describes an application of the logic programming paradigm to large-scale comparison of complete microbial genomes each containing four-million amino acid characters and approximately two thousand genes. We present algorithms and a Sicstus Prolog based implementation to model genome comparisons as bipartite graph matching to identify orthologs — genes across different genomes with the same function — and groups of orthologous genes — orthologous genes in close proximity, and gene duplications. The application is modular, and integrates logic programming with Unix-based programming and a Prolog based text-processing library developed during this project. The scheme has been successfully applied to compare eukaryotes such as yeast. The data generated by the software is being used by microbiologists and computational biologists to understand the regulation mechanisms and the metabolic pathways in microbial genomes.

This research was supported in part by Research Council grant, Kent State University, Kent, Ohio, USA and Deutsche Forschungsgemeinschaft — The German Federal Agency

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Author information

Authors and Affiliations

  1. Department of Mathematics and Computer Science, Kent State University, Kent, OH, 44242, USA

    Arvind K. Bansal

  2. Computer Informatics Division, European Molecular Biology Laboratory, Meyerhofstr 1, Postfach 10 22 09, 69012, Heidelberg, Germany

    Peer Bork

Authors
  1. Arvind K. Bansal
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  2. Peer Bork
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Corresponding author

Correspondence to Arvind K. Bansal .

Editor information

Editors and Affiliations

  1. Department of Computer Science, New Mexico State University, Box 30001, New Science Hall (MS CS) Stewart Street, Las Cruces, NM, 88003, USA

    Gopal Gupta

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© 1998 Springer-Verlag Berlin Heidelberg

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Bansal, A.K., Bork, P. (1998). Applying Logic Programming to Derive Novel Functional Information of Genomes. In: Gupta, G. (eds) Practical Aspects of Declarative Languages. PADL 1999. Lecture Notes in Computer Science, vol 1551. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-49201-1_19

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  • DOI: https://doi.org/10.1007/3-540-49201-1_19

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-65527-5

  • Online ISBN: 978-3-540-49201-6

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