PathAligner: Metabolic Pathway Retrieval and Alignment

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

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
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
Applied Bioinformatics
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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, Ming, and Hofestädt, Ralf. 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.

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PMID: 27112575
Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms.
Ortegon P, Poot-Hernández AC, Perez-Rueda E, Rodriguez-Vazquez K., Comput Struct Biotechnol J 13(), 2015
PMID: 25973143
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Poot-Hernandez AC, Rodriguez-Vazquez K, Perez-Rueda E., BMC Genomics 16(), 2015
PMID: 26578309
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
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
Automatic Perception of Chemical Similarities Between Metabolic Pathways.
Latino DA, Aires-de-Sousa J., Mol Inform 31(2), 2012
PMID: 27476958
Metabolic network alignment in large scale by network compression.
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PMID: 22536900
SAGA: a subgraph matching tool for biological graphs.
Tian Y, McEachin RC, Santos C, States DJ, Patel JM., Bioinformatics 23(2), 2007
PMID: 17110368

26 References

Daten bereitgestellt von Europe PubMed Central.

A minimal gene set for cellular life derived by comparison of complete bacterial genomes.
Mushegian AR, Koonin EV., Proc. Natl. Acad. Sci. U.S.A. 93(19), 1996
PMID: 8816789
Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.
Bono H, Ogata H, Goto S, Kanehisa M., Genome Res. 8(3), 1998
PMID: 9521924
PathFinder: reconstruction and dynamic visualization of metabolic pathways.
Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R., Bioinformatics 18(1), 2002
PMID: 11836220
Representation of function: the next step.
Overbeek R, Larsen N, Smith W, Maltsev N, Selkov E., Gene 191(1), 1997
PMID: 9210599
A reconstruction of the metabolism of Methanococcus jannaschii from sequence data.
Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman WB., Gene 197(1-2), 1997
PMID: 9332394
Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.
Nakao M, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M., Genome Inform Ser Workshop Genome Inform 10(), 1999
PMID: 11072346
Metabolic modeling of microbial strains in silico.
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO., Trends Biochem. Sci. 26(3), 2001
PMID: 11246024
Representing and analysing molecular and cellular function using the computer.
van Helden J, Naim A, Mancuso R, Eldridge M, Wernisch L, Gilbert D, Wodak SJ., Biol. Chem. 381(9-10), 2000
PMID: 11076023
Computation with the KEGG pathway database.
Ogata H, Goto S, Fujibuchi W, Kanehisa M., BioSystems 47(1-2), 1998
PMID: 9715755
Reconstruction of metabolic networks using incomplete information.
Gaasterland T, Selkov E., Proc Int Conf Intell Syst Mol Biol 3(), 1995
PMID: 7584429
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar T, Schuster S, Snel B, Huynen M, Bork P., Biochem. J. 343 Pt 1(), 1999
PMID: 10493919
A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy.
Tohsato Y, Matsuda H, Hashimoto A., Proc Int Conf Intell Syst Mol Biol 8(), 2000
PMID: 10977098
Phylogenetic analysis of metabolic pathways.
Forst CV, Schulten K., J. Mol. Evol. 52(6), 2001
PMID: 11443351
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL., Nucleic Acids Res. 31(1), 2003
PMID: 12519940
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M., Nucleic Acids Res. 31(1), 2003
PMID: 12520024
BRENDA, enzyme data and metabolic information.
Schomburg I, Chang A, Schomburg D., Nucleic Acids Res. 30(1), 2002
PMID: 11752250
The KEGG databases at GenomeNet.
Kanehisa M, Goto S, Kawashima S, Nakaya A., Nucleic Acids Res. 30(1), 2002
PMID: 11752249
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E., Nucleic Acids Res. 28(1), 2000
PMID: 10592199
The MetaCyc Database.
Karp PD, Riley M, Paley SM, Pellegrini-Toole A., Nucleic Acids Res. 30(1), 2002
PMID: 11752254
PIR: a new resource for bioinformatics.
McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH., Bioinformatics 16(3), 2000
PMID: 10869023
The Protein Data Bank.
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C., Acta Crystallogr. D Biol. Crystallogr. 58(Pt 6 No 1), 2002
PMID: 12037327
TRANSFAC: transcriptional regulation, from patterns to profiles.
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E., Nucleic Acids Res. 31(1), 2003
PMID: 12520026
TRANSPATH: an integrated database on signal transduction and a tool for array analysis.
Krull M, Voss N, Choi C, Pistor S, Potapov A, Wingender E., Nucleic Acids Res. 31(1), 2003
PMID: 12519957

Gansner, Softw Pract Exper 30(11), 2000
BioDataServer: a SQL-based service for the online integration of life science data.
Freier A, Hofestadt R, Lange M, Scholz U, Stephanik A., In Silico Biol. (Gedrukt) 2(2), 2002
PMID: 12066840

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