PathAligner: Metabolic pathway retrieval and alignment

Applied Bioinformatics

Volumn 3, Issue 4, 2004, Pages 241-252

  Chen, Ming ^a   Hofestädt, Ralf ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ARTICLE; DATA BASE; GENE SEQUENCE; INFORMATION PROCESSING; INTERNET; MATHEMATICAL COMPUTING; METABOLISM;

ALGORITHMS; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; GENE EXPRESSION REGULATION; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; PROTEOME; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 22144433573     PISSN: 11755636     EISSN: None     Source Type: Journal    
DOI: 10.2165/00822942-200403040-00006     Document Type: Article

References (29)

1. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 1996; 93 (19): 10268-73
2. Bono H, Ogata H, Goto S, et al. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 1998; 8: 203-10
3. Goesmann A, Haubrock M, Meyer F, et al. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics 2002; 18: 124-9
4. Overbeek R, Larsen N, Smith W, et al. Representation of function: the next step. Gene 1997; 191: GC1-9
5. Selkov E, Maltsev N, Olsen GJ, et al. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 1997; 197: GC11-26
6. Nakao M, Bono H, Kawashima S, et al. Genome-scale gene expression analysis and pathway reconstruction in KEGG. Genome Inform Ser Workshop Genome Inform 1999; 10: 94-103
7. Covert MW, Schilling CH, Famili I, et al. Metabolic modeling of microbial strains in silico. Trends Biochem Sci 2001; 26 (3): 179-86
8. van Helden J, Naim A, Mancuso R, et al. Representing and analysing molecular and cellular function using the computer. Biol Chem 2000; 381 (9-10): 921-35
9. Ogata H, Goto S, Fujibuchi W, et al. Computation with the KEGG pathway database. Biosystems 1998; 47: 119-28
10. Gaasterland T, Selkov E. Reconstruction of metabolic networks using incomplete information. Proc Int Conf Intell Syst Mol Biol 1995; 3: 127-35
11. Dandekar T, Schuster S, Snel B, et al. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J 1999; 343: 115-24
12. Tohsato Y, Matsuda H, Hashimoto A. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Proc Int Conf Intell Syst Mol Biol 2000; 8: 376-83
13. Forst CV, Schulten K. Phylogenetic analysis of metabolic pathways. J Mol Evol 2001; 52: 471-89
14. Liao L, Kim S, Tomb JF. Genome comparisons based on profiles of metabolic pathways. Sixth International Conference on Knowledge-Based Intelligent Information and Engineering Systems (KES 2002); 2002 Sep 16-18; Crema, Italy. Amsterdam: IOS Press, 2002: 469-76
15. Forst CV, Schulten K. Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J Comput Biol 1999; 6: 343-60
16. Webb EC. Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. New York: Academic Press, 1992
17. Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res 2003; 31 (1): 23-7
18. Boeckmann B, Bairoch A, Apweiler R, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003; 31 (1): 365-70
19. Schomburg I, Chang A, Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Res 2002; 30 (1): 47-9
20. Kanehisa M, Goto S, Kawashima S, et al. The KEGG databases at GenomeNet. Nucleic Acids Res 2002; 30 (1): 42-6
21. Overbeek R, Larsen N, Pusch GD, et al. WIT: integrated system for high throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res 2000; 28 (1): 123-5
22. Karp PD, Riley M, Paley SM, et al. The MetaCyc Database. Nucleic Acids Res 2002; 30 (1): 59-61
23. McGarvey PB, Huang H, Barker WC, et al. PIR: a new resource for bioinformatics. Bioinformatics 2000; 16 (3): 290-1
24. Berman HM, Battistuz T, Bhat TN, et al. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002; 58: 899-907
25. Matys V, Fricke E, Geffers R, et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003; 31 (1): 374-8
26. Krull M, Voss N, Choi C, et al. TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res 2003; 31 (1): 97-100
27. Gansner ER, North SC. An open graph visualization system and its applications to software engineering. Softw Pract Exper 2000; 30 (11): 1203-33
28. Chen M, Freier A, Köhler J, et al. The biology Petri net markup language. In: Lecture notes in informatics: Proceedings of Promise2002. 2002 Oct 9-11; Potsdam, Germany. Vol. 21. Bonn: Bonner Köllen Verlag: 150-61
29. Freier A, Hofestädt R, Lange M, et al. BioDataServer: a SQL-based service for the online integration of life science data. In Silico Biol 2002; 2: 37-57