PathAligner: Metabolic Pathway Retrieval and Alignment

Chen M, Hofestädt R (2004)
Applied Bioinformatics 3(4): 241-252.

Journal Article | Published | English

No fulltext has been uploaded

Author
;
Abstract
MOTIVATION: Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways at both the genomic and the metabolic levels. Retrieving metabolic pathways from current biological data sources, reconstructing metabolic pathways from rudimentary pathway components, and aligning metabolic pathways with each other are major tasks. Our motivation was to develop a conceptual framework and computational system that allows the retrieval of metabolic pathway information and the processing of alignments to reveal the similarities between metabolic pathways. RESULTS: PathAligner extracts metabolic information from biological databases via the Internet and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites etc. It provides an easy-to-use interface to retrieve, display and manipulate metabolic information. PathAligner also provides an alignment method to compare the similarity between metabolic pathways. AVAILABILITY: PathAligner is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner.
Publishing Year
ISSN
PUB-ID

Cite this

Chen M, Hofestädt R. PathAligner: Metabolic Pathway Retrieval and Alignment. Applied Bioinformatics. 2004;3(4):241-252.
Chen, M., & Hofestädt, R. (2004). PathAligner: Metabolic Pathway Retrieval and Alignment. Applied Bioinformatics, 3(4), 241-252.
Chen, M., and Hofestädt, R. (2004). PathAligner: Metabolic Pathway Retrieval and Alignment. Applied Bioinformatics 3, 241-252.
Chen, M., & Hofestädt, R., 2004. PathAligner: Metabolic Pathway Retrieval and Alignment. Applied Bioinformatics, 3(4), p 241-252.
M. Chen and R. Hofestädt, “PathAligner: Metabolic Pathway Retrieval and Alignment”, Applied Bioinformatics, vol. 3, 2004, pp. 241-252.
Chen, M., Hofestädt, R.: PathAligner: Metabolic Pathway Retrieval and Alignment. Applied Bioinformatics. 3, 241-252 (2004).
Chen, Ming, and Hofestädt, Ralf. “PathAligner: Metabolic Pathway Retrieval and Alignment”. Applied Bioinformatics 3.4 (2004): 241-252.
This data publication is cited in the following publications:
This publication cites the following data publications:

5 Citations in Europe PMC

Data provided by Europe PubMed Central.

The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria.
Poot-Hernandez AC, Rodriguez-Vazquez K, Perez-Rueda E., BMC Genomics 16(), 2015
PMID: 26578309
MIMO: an efficient tool for molecular interaction maps overlap.
Di Lena P, Wu G, Martelli PL, Casadio R, Nardini C., BMC Bioinformatics 14(), 2013
PMID: 23672344
Genome-scale metabolic model in guiding metabolic engineering of microbial improvement.
Xu C, Liu L, Zhang Z, Jin D, Qiu J, Chen M., Appl. Microbiol. Biotechnol. 97(2), 2013
PMID: 23188456
SAGA: a subgraph matching tool for biological graphs.
Tian Y, McEachin RC, Santos C, States DJ, Patel JM., Bioinformatics 23(2), 2007
PMID: 17110368

Export

0 Marked Publications

Open Data PUB

Sources

PMID: 15702955
PubMed | Europe PMC

Search this title in

Google Scholar