{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:15:05Z","timestamp":1762521305704},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In their article entitled \u2018Can sugars be produced from fatty acids? A test case for pathway analysis tools\u2019 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. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the \u2018assessment\u2019 is restricted to two study cases; (iii) 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.<\/jats:p>\n               <jats:p>Contact: \u00a0kfaust@ulb.ac.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp557","type":"journal-article","created":{"date-parts":[[2009,9,24]],"date-time":"2009-09-24T01:29:48Z","timestamp":1253755788000},"page":"3202-3205","source":"Crossref","is-referenced-by-count":9,"title":["In response to \u2018Can sugars be produced from fatty acids? A test case for pathway analysis tools\u2019"],"prefix":"10.1093","volume":"25","author":[{"given":"Karoline","family":"Faust","sequence":"first","affiliation":[{"name":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Didier","family":"Croes","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacques","family":"van Helden","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,9,23]]},"reference":[{"key":"2023013112193201200_B1","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1101\/gr.1212003","article-title":"In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism","volume":"13","author":"Arita","year":"2003","journal-title":"Genome Res."},{"key":"2023013112193201200_B2","volume-title":"Biochemistry.","author":"Berg","year":"2002"},{"key":"2023013112193201200_B3","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1093\/bioinformatics\/btn360","article-title":"MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization","volume":"24","author":"Blum","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112193201200_B4","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1128\/AEM.71.2.713-720.2005","article-title":"Kinetic studies and biochemical pathway analysis of anaerobic poly-(R)-3-hydroxybutyric acid synthesis in Escherichia coli","volume":"71","author":"Carlson","year":"2004","journal-title":"Appl.Environ. 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