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The university of minnesota biocatalysis/biodegradation database: Emphasizing enzymes
- Nucleic Acids Res
, 2003
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Cases I: Bionemo: molecular information on biodegradation metabolism
- Nucleic Acids Res 2009, 37(Database issue):D598–602
"... metabolism ..."
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Original article
"... AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics ..."
Abstract
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AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics
case for pathway analysis tools”
"... Motivation: In their article entitled “Can sugars be produced from fatty acids? A test case for pathway analysis tools ” de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G ..."
Abstract
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Motivation: In their article entitled “Can sugars be produced from fatty acids? A test case for pathway analysis tools ” de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case (de Figueiredo, et al., 2008). We think that this article is biased for three reasons: (1) The metabolic networks used as input for the respective tools were of very different sizes; (2) the “assessment ” is restricted to two study cases; (3) developers are inherently more skilled to use their own tools than those developed by other people. We extended the analyses led by de Figueiredo and clearly show that the apparent superior performance of their tool (METATOOL) is partly due to the differences in input network sizes. We also see a conceptual problem in the comparison of tools that serve different purposes. In our opinion, metabolic path finding and elementary mode analysis are answering different biological questions, and should be considered as complementary rather than competitive approaches. 1
