ENZYME-SPECIFIC PROFILES for metabolic pathway prediction

PRIAM: PRofils pour l'Identification Automatique du Métabolisme


Clotilde Claudel-Renard, Claude Chevalet, Thomas Faraut and Daniel Kahn / Enzyme-specific profiles for genome annotation: PRIAM Nucleic Acids Research, 2003, Vol. 31, No. 22 6633-6639

The prediction of metabolic pathways of many species is becoming possible with the advent of complete sequence genomes, on the basis of the identification of enzyme coding genes.
PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.
PRIAM relies on sets of position-specific score matrices (PSSMs) automatically tailored for each ENZYME entry. The whole Swiss-Prot database has been used to parameterise and to assess the method.
As an example, PRIAM was applied to predict metabolic pathways from the complete genome of the nitrogen fixing bacterium Sinorhizobium meliloti and on the plant pathogen Ralstonia solanacearum. The results of this automated annotation method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of predicted metabolic pathways and to highlight potentially missing enzymes.

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