CoherenZy

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CoherenZy is a collection of modules (FamCOH, FamSplit, TM and ML) being developed to ascertain the coherency of functional annotation of carbohydrate enzyme families.

CoherenZy use as case-study CAZy, a database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This work is being develop in collaboration with team the Glycogenomics research team that created and currently maintains and curates this database.

Modules:

FamCOH (1): Uses enzyme families' functional annotations as input to measures the family functional annotation coherence, that is, the level of functional relatedness between the family members, according to its annotations.

FamSplit (2): This module proposes segregation of enzyme families into more closely functionally related sub-families (according to the FamCOH).

ML (3): Machine learning classifier to classify novel sequences into existing enzyme (sub-)families.

TM (4): Provides text mining methods to enrich sub-annotated families.



CoherenZy modular system
Research Team


Funding


  • Period: 1-Mar-2008 to 28-Feb-2013
  • Funding:
    • SFRH/BD/48035/2008, Doctoral research scholarship for Hugo Bastos
    • Acções Integradas Luso-Francesas - 2010. Acção nº F-TC-3/10


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Publications


Document | BibTeX source
Hugo Bastos, Francisco Couto, Pedro M. Coutinho, Exploring Gene Ontology relationships in Enzyme Families: An application to Polysaccharide Lyases (as a poster).9th Carbohydrate Bioengineering Meeting p. 67, May, 2011.

DOI | BibTeX source
P.M. Coutinho, C. Rancurel, M. Stam, T. Bernard, Francisco Couto, E.G.J. Danchin, B. Henrissat: Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases. in: Bioinformatics for Glycobiology and Glycomics. Wiley. 2009.

Document | BibTeX source
Hugo Bastos, Tiago Grego, Francisco Couto, Pedro M. Coutinho, Enzyme family coherence assessment: validation and prediction.JB'2009 - Challenges in Bioinformatics p. 26-30, Lisbon, Portugal, November, 2009.


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