Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (22)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Goesmann, A.
Right arrow Articles by Giegerich, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Goesmann, A.
Right arrow Articles by Giegerich, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 1 2002
Pages 124-129
© 2002 Oxford University Press

PathFinder: reconstruction and dynamic visualization of metabolic pathways

Alexander Goesmann 1, Martin Haubrock 2, Folker Meyer 1, Jörn Kalinowski 1 and Robert Giegerich 3

1 Center for Genome Research, Department of Genetics, Bielefeld University, 33594 Bielefeld, Germany
2 Biobase GmbH, Mascheroder Weg 1B, 38114 Braunschweig, Germany
3 Technische Fakultät, Bielefeld University, 33594 Bielefeld, Germany

Received on January 29, 2001 ; revised on July 5, 2001 ; accepted on July 30, 2001

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.

Availability: The software PathFinder will be made available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/pathfinder/. The source code is available upon request and will eventually be released under GPL.

Contact: Alexander.Goesmann{at}Genetik.Uni-Bielefeld.DE


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
C. Choi, R. Munch, S. Leupold, J. Klein, I. Siegel, B. Thielen, B. Benkert, M. Kucklick, M. Schobert, J. Barthelmes, et al.
SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D533 - D537.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Baitaluk, M. Sedova, A. Ray, and A. Gupta
BiologicalNetworks: visualization and analysis tool for systems biology.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W466 - W471.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Mlecnik, M. Scheideler, H. Hackl, J. Hartler, F. Sanchez-Cabo, and Z. Trajanoski
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W633 - W637.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. Li and H. Kurata
A grid layout algorithm for automatic drawing of biochemical networks
Bioinformatics, May 1, 2005; 21(9): 2036 - 2042.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Holford, N. Li, P. Nadkarni, and H. Zhao
VitaPad: visualization tools for the analysis of pathway data
Bioinformatics, April 15, 2005; 21(8): 1596 - 1602.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Meyer, A. Goesmann, A. C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, et al.
GenDB--an open source genome annotation system for prokaryote genomes
Nucleic Acids Res., April 15, 2003; 31(8): 2187 - 2195.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.