ENZYME-SPECIFIC PROFILES for metabolic pathway prediction
PRIAM: PRofils pour l'Identification Automatique du Métabolisme
Clotilde CLAUDEL-RENARD, Claude CHEVALET, Thomas FARAUT, Daniel KAHN
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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- October 2001(Enzyme rel. 27.0)
- July 2003 (Enzyme rel. 31)
- July 2004 (Enzyme rel. 35)
- July 2005 release 2 (Enzyme rel. 38)
- July 2006 (Enzyme rel. 39)
- September 2008 (Enzyme rel. of 02-Sep-2008)
- November 2008 (Enzyme rel. of 25-Nov-2008)
- June 2009 (Enzyme rel. of 16-Jun-2009)
- August 2010 (Enzyme rel. of 10-Aug-2010)
- November 2010 (Enzyme rel. of 30-Nov-2010)
- May 2011 (Enzyme rel. of 31-May-2011)
- October 2011 (Enzyme rel. of 19-October-2011)
- September 2012 (Enzyme rel. of 05-September-2012)
- March 2013 (Enzyme rel. of 06-March-2013)
- February 2014 (Enzyme rel. of 19-Feb-2014)
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