title: FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology.
abstract: BACKGROUND
  More and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth.
  
  
  METHODS
  FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.fr.
  
  
  CONCLUSIONS
  As more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.
authors.affiliation: Institut de Génétique et de Microbiologie, Université Paris-Sud 11, CNRS UMR 8621, Bâtiment 400, 91405 Orsay Cedex, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Grossetête
authors.forename: Bernard
authors.initials: B
authors.lastname: Labedan
authors.forename: Olivier
authors.initials: O
authors.lastname: Lespinet
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030562:Databases, Protein; D005658:Fungi / Q000235:genetics; D016681:Genome, Fungal; D053858:Metabolic Networks and Pathways