GenDB - An open source genome annotation system for prokaryote genomes

Nucleic Acids Research

Volumn 31, Issue 8, 2003, Pages 2187-2195

  Meyer, Folker ^a   Goesmann, Alexander ^a   McHardy, Alice C ^a   Bartels, Daniela ^a   Bekel, Thomas ^a   Clausen, Jörn ^a   Kalinowski, Jörn ^a   Linke, Burkhard ^a   Rupp, Oliver ^a   Giegerich, Robert ^a   Pühler, Alfred ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; GENE SEQUENCE; GENETIC DATABASE; GENOME ANALYSIS; INFORMATION RETRIEVAL; PRIORITY JOURNAL; PROKARYOTE; AMINO ACID SEQUENCE; BACTERIAL GENOME; BACTERIUM; BIOLOGY; GENETICS; GENOME; INTERNET; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROKARYOTIC CELL; SEQUENCE HOMOLOGY;

PROKARYOTA;

AMINO ACID SEQUENCE; BACTERIA; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENOME; GENOME, BACTERIAL; INTERNET; MOLECULAR SEQUENCE DATA; PROKARYOTIC CELLS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0037561991     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg312     Document Type: Article

References (20)

1. Gaasterland,T. and Sensen,C.W. (1996) MAGPIE: automated genome interpretation. Trends Genet., 12, 76-78.
2. Andrade,M.A., Brown,N.P., Leroy,C., Hoersch,S., de Daruvar,A., Reich,C., Franchini,A., Tamames,J., Valencia,A., Ouzounis,C. and Sander,C. (1999) Automated genome sequence analysis and annotation. Bioinformatics, 15, 391-412.
3. Frishman,D., Albermann,K., Hani,J., Heumann,K., Metanomski,A., Zollner,A. and Mewes,H.W. (2001) Functional and structural genomics using PEDANT. Bioinformatics, 17, 44-57.
4. Overbeek,R., Larsen,N., Pusch,G.D., D'Souza,M., Selkov,E., Kyrpides,N., Fonstein,M., Maltsev,N. and Selkov,E. (2002) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res., 28, 123-125.
5. Rutherford,K.M., Parkhill,J., Crook,J., Horsnell,T., Rice,P., Rajandream,M.-A. and Barrell,B. (2000) Artemis: sequence visualisation and annotation. Bioinformatics, 16, 944-945.
6. Overbeck,R., Fontstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D.R., Durbin,R., Falquet,L., Fleischmann,W., Gouzy,J., Hermjakob,H., Hulo,N., Jonassen,I., Kahn,D., Kanapin,A., Karavidopoulou,Y., Lopez,R., Marx,B., Mulder,T.M., Oinn,N.J., Pagni,M., Servant,F., Sigrist,C.J.A. and Zdobnov,E.M. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
9. Etzold,T. and Argos,P. (1993) SRS: an indexing and retrieval tool for flat file data libraries. CABIOS, 9, 49-57.
10. Goesmann,A., Haubrock,M., Meyer,F., Kalinowski,J. and Giegerich,R. (2002) Pathfinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics, 18, 124-129.
11. Delcher,A.L., Harmon,D., Kasif,S., White,O. and Salzberg,S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
12. Badger,H. and Olsen,G.J. (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol., 16, 512-524.
13. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
14. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
15. Henikoff,S. and Henikoff,J.G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res., 19, 6565-6572.
16. Sonnhammer,E.L.L., von Heijne,G. and Krogh,A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In Glasgow,J., Littlejohn,T., Major,R., Lathrop,F., Sankoff,D. and Sensen,C. (eds), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 175-182.
17. Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
18. Galibert,F., Finan,T.M., Long,S.R., Pühler,A., Abola,P., Ampe,F., Barloy-Hubler,F., Barnett,M.J., Becker,A., Boistard,P., Bothe,G., Boutry,M., Bowser,L., Buhrmester,J., Cadieu,E., Capela,D., Chain,P., Cowie,A., Davis,R.W., Dreano,S., Federspiel,N.A., Fisher,R.F., Gloux,S., Godrie,T., Goffeau,A., Golding,B., Gouzy,J., Gurjal,M., Hernandez-Lucas,I., Hong,A., Huizar,L., Hyman,R.W., Jones,T., Kahn,D., Kahn,M.L., Kalman,S., Keating,D.H., Kiss,E., Komp,C., Lelaure,V., Masuy,D., Palm,C., Peck,M.C., Pohl,T.M., Portetelle,D., Purnelle,B., Ramsperger,U., Surzycki,R., Thebault,P., Vandenbol,M., Vorhölter,F.J., Weidner,S., Wells,D.H., Wong,K., Yeh,K.C. and Batut,J. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science, 29, 668-672.
19. Tauch,A., Schneiker,S., Selbitschka,W., Pühler,A., van Overbeek,L.S., Smalla,K., Thomas,C.M., Bailey,M.J., Forney,L.J., Weightman,A., Ceglowski,P., Pembroke,T., Tietze,E., Schroder,G., Lanka,E. and van Elsas,J.D. (2002) The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. Microbiology, 148, 1637-1653.
20. Tauch,A., Schlüter,A., Bischoff,N., Goesmann,A., Meyer,F. and Pühler,A. (2002) The 79,370bp conjugative plasmid pb4 consists of an incp-beta backbone loaded with a chromate resistance transposon, the stra-strb streptomycin resistance gene pair, the oxacillinase gene bla(nps-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol. Gen. Genomics, 268, 570-584.