title: PathFinder: reconstruction and dynamic visualization of metabolic pathways.
abstract: BACKGROUND
  Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed.
  
  
  RESULTS
  PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.
authors.affiliation: Center for Genome Research, Department of Genetics, Bielefeld University, 33594 Bielefeld, Germany. Alexander.Goesmann@Genetik.Uni-Bielefeld.DE
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Martin
authors.initials: M
authors.lastname: Haubrock
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Jörn
authors.initials: J
authors.lastname: Kalinowski
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003628:Database Management Systems; D015870:Gene Expression; D005798:Genes, Bacterial; D008239:Lysine / Q000096:biosynthesis; D008660:Metabolism; D012984:Software
chemical_list: D008239:Lysine