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Automated Enzyme Classification by Formal Concept Analysis

  • François Coste
  • Gaëlle Garet
  • Agnès Groisillier
  • Jacques Nicolas
  • Thierry Tonon
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8478)

Abstract

Enzymes are macro-molecules (linear sequences of linked molecules) with a catalytic activity that make them essential for any biochemical reaction. High throughput genomic techniques give access to the sequence of new enzymes found in living organisms. Guessing the enzyme’s functional activity from its sequence is a crucial task that can be approached by comparing the new sequences with those of already known enzymes labeled by a family class. This task is difficult because the activity is based on a combination of small sequence patterns and sequences greatly evolved over time. This paper presents a classifier based on the identification of common subsequence blocks between known and new enzymes and the search of formal concepts built on the cross product of blocks and sequences for each class. Since new enzyme families may emerge, it is important to propose a first classification of enzymes that cannot be assigned to a known family. FCA offers a nice framework to set the task as an optimization problem on the set of concepts. The classifier has been tested with success on a particular set of enzymes present in a large variety of species, the haloacid dehalogenase superfamily.

Keywords

bioinformatics protein classification FCA application 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • François Coste
    • 1
  • Gaëlle Garet
    • 1
  • Agnès Groisillier
    • 2
  • Jacques Nicolas
    • 1
  • Thierry Tonon
    • 2
  1. 1.Irisa / Inria RennesRennes cedexFrance
  2. 2.Integrative Biology of Marine ModelsSorbonne Universités, UPMC Univ Paris 06, UMR 8227, and CNRS, UMR 8227Roscoff cedexFrance

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