Nucleic Acids Research, 2004, Vol. 32, Database issue D273-D276
© 2004 Oxford University Press
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
Information Génomique and Structurale, CNRS-UPR 2589, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
*To whom correspondence should be addressed. Tel: +33 4 91 16 46 04; Fax: +33 4 91 16 45 49; Email: karsten.suhre{at}igs.cnrs-mrs.fr
FusionDB (http://igs-server.cnrs-mrs.fr/FusionDB/) constitutes a resource dedicated to in-depth analysis of bacterial and archaeal gene fusion events. Such events can provide the ‘Rosetta stone’ in the search for potential protein–protein interactions, as well as metabolic and regulatory networks. However, the false positive rate of this approach may be quite high, prompting a detailed scrutiny of putative gene fusion events. FusionDB readily provides much of the information required for that task. Moreover, FusionDB extends the notion of gene fusion from that of a single gene to that of a family of genes by assembling pairs of genes from different genomes that belong to the same Cluster of Orthogonal Groups (COG). Multiple sequence alignments and phylogenetic tree reconstruction for the N- and C-terminal parts of these ‘COG fusion’ events are provided to distinguish single and multiple fusion events from cases of gene fission, pseudogenes and other false positives. Finally, gene fusion events with matches to known structures of heterodimers in the Protein Data Bank (PDB) are identified and may be visualized. FusionDB is fully searchable with access to sequence and alignment data at all levels. A number of different scores are provided to easily differentiate ‘real’ from ‘questionable’ cases, especially when larger database searches are performed. FusionDB is cross-linked with the ‘Phylogenomic Display of Bacterial Genes’ (PhydBac) online web server. Together, these servers provide the complete set of information required for in-depth analysis of non-homology-based gene function attribution.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. Muralla, E. Chen, C. Sweeney, J. A. Gray, A. Dickerman, B. J. Nikolau, and D. Meinke A Bifunctional Locus (BIO3-BIO1) Required for Biotin Biosynthesis in Arabidopsis Plant Physiology, January 1, 2008; 146(1): 60 - 73. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Nakamura, T. Itoh, and W. Martin Rate and Polarity of Gene Fusion and Fission in Oryza sativa and Arabidopsis thaliana Mol. Biol. Evol., January 1, 2007; 24(1): 110 - 121. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Field, E. J. Feil, and G. A. Wilson Databases and software for the comparison of prokaryotic genomes Microbiology, July 1, 2005; 151(7): 2125 - 2132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. A. Stover, A. R. O. Cavalcanti, A. J. Li, B. C. Richardson, and L. F. Landweber Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms Mol. Biol. Evol., July 1, 2005; 22(7): 1539 - 1542. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Gopal, I. Borovok, A. Ofer, M. Yanku, G. Cohen, W. Goebel, J. Kreft, and Y. Aharonowitz A Multidomain Fusion Protein in Listeria monocytogenes Catalyzes the Two Primary Activities for Glutathione Biosynthesis J. Bacteriol., June 1, 2005; 187(11): 3839 - 3847. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Pasek, A. Bergeron, J.-L. Risler, A. Louis, E. Ollivier, and M. Raffinot Identification of genomic features using microsyntenies of domains: Domain teams Genome Res., June 1, 2005; 15(6): 867 - 874. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Choi, Y. Ma, J.-H. Choi, and S. Kim PLATCOM: a Platform for Computational Comparative Genomics Bioinformatics, May 15, 2005; 21(10): 2514 - 2516. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. K. Philip, C. J. Creevey, and J. O. McInerney The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa Mol. Biol. Evol., May 1, 2005; 22(5): 1175 - 1184. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. M. Harvat, Y.-M. Zhang, C. V. Tran, Z. Zhang, M. W. Frank, C. O. Rock, and M. H. Saier Jr. Lysophospholipid Flipping across the Escherichia coli Inner Membrane Catalyzed by a Transporter (LplT) Belonging to the Major Facilitator Superfamily J. Biol. Chem., March 25, 2005; 280(12): 12028 - 12034. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Inbar, H. J. Wolfson, and R. Nussinov Multiple Docking for Protein Structure Prediction The International Journal of Robotics Research, February 1, 2005; 24(2-3): 131 - 150. [Abstract] [PDF]
|
|
|
|
 |
|
 M. Y. Galperin and E. V. Koonin 'Conserved hypothetical' proteins: prioritization of targets for experimental study Nucleic Acids Res., October 12, 2004; 32(18): 5452 - 5463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Enault, K. Suhre, O. Poirot, C. Abergel, and J.-M. Claverie Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis Nucleic Acids Res., July 1, 2004; 32(suppl_2): W336 - W339. [Abstract] [Full Text] [PDF]
|
|