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Trends Parasitol. 2009 Jan;25(1):37-43. doi: 10.1016/j.pt.2008.08.012. Epub 2008 Nov 3.

Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium.

Author information

1
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 91904, Israel. hagai@vms.huji.ac.il

Abstract

The functional reconstruction of metabolic pathways from an annotated genome is a tedious and demanding enterprise. Automation of this endeavor using bioinformatics algorithms could cope with the ever-increasing number of sequenced genomes and accelerate the process. Here, the manual reconstruction of metabolic pathways in the functional genomic database of Plasmodium falciparum--Malaria Parasite Metabolic Pathways--is described and compared with pathways generated automatically as they appear in PlasmoCyc, metaSHARK and the Kyoto Encyclopedia for Genes and Genomes. A critical evaluation of this comparison discloses that the automatic reconstruction of pathways generates manifold paths that need an expert manual verification to accept some and reject most others based on manually curated gene annotation.

PMID:
18986839
DOI:
10.1016/j.pt.2008.08.012
[Indexed for MEDLINE]

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