PathFinder: reconstruction and dynamic visualization of metabolic pathways

Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R (2002)
BIOINFORMATICS 18(1): 124-129.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Motivation: 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.
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Zeitschriftentitel
BIOINFORMATICS
Band
18
Zeitschriftennummer
1
Seite
124-129
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Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS. 2002;18(1):124-129.
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., & Giegerich, R. (2002). PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS, 18(1), 124-129. doi:10.1093/bioinformatics/18.1.124
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., and Giegerich, R. (2002). PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS 18, 124-129.
Goesmann, A., et al., 2002. PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS, 18(1), p 124-129.
A. Goesmann, et al., “PathFinder: reconstruction and dynamic visualization of metabolic pathways”, BIOINFORMATICS, vol. 18, 2002, pp. 124-129.
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., Giegerich, R.: PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS. 18, 124-129 (2002).
Goesmann, Alexander, Haubrock, Martin, Meyer, Folker, Kalinowski, Jörn, and Giegerich, Robert. “PathFinder: reconstruction and dynamic visualization of metabolic pathways”. BIOINFORMATICS 18.1 (2002): 124-129.

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GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A., Nucleic Acids Res 31(8), 2003
PMID: 12682369

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