Nucleic Acids Research, 2003, Vol. 31, No. 1 187-189
© 2003 Oxford University Press
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, ‘Rovira i Virgili’ University, Pl Imperial Tàrraco 1, E-43005 Tarragona, Spain
*To whom correspondence should be addressed. Tel: +34 977559565; Fax: +34 977558232; Email: vallve{at}quimica.urv.es
ABSTRACT
The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database contains 88 bacterial and archaeal complete genomes, including multiple chromosomes and strains. For each genome, the database provides statistical parameters for all the genes, as well as averages and standard deviations of G+C content, codon usage, relative synonymous codon usage and amino-acid content. It also provides information about correspondence analyses of the codon usage, plus lists of extraneous group of genes in terms of G+C content and lists of putatively acquired genes. With this information, researchers can explore the G+C content and codon usage of a gene when they find incongruities in sequence-based phylogenetic trees. A search engine that allows searches for gene names or keywords for a specific organism is also available. HGT-DB is freely accessible at http://www.fut.es/~debb/HGT.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G.-Q. Hu, J.-T. Guo, Y.-C. Liu, and H. Zhu MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction Bioinformatics, July 15, 2009; 25(14): 1843 - 1845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. A. Findlay and R. J. Redfield Coevolution of DNA Uptake Sequences and Bacterial Proteomes Gen Biol Evol, June 22, 2009; 2009(0): 45 - 55. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F.-B. Guo and J.-B. Yuan Codon Usages of Genes on Chromosome, and Surprisingly, Genes in Plasmid are Primarily Affected by Strand-specific Mutational Biases in Lawsonia intracellularis DNA Res, April 1, 2009; 16(2): 91 - 104. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Suzuki, M. Sota, C. J. Brown, and E. M. Top Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes Nucleic Acids Res., December 1, 2008; 36(22): e147 - e147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Suzuki, C. J. Brown, L. J. Forney, and E. M. Top Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria DNA Res, December 1, 2008; 15(6): 357 - 365. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-W. Jiang, K.-L. Lin, and C. L. Lu OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes Nucleic Acids Res., July 1, 2008; 36(suppl_2): W475 - W480. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Peng Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival Microbiology, February 1, 2008; 154(2): 383 - 391. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Puigbo, A. Romeu, and S. Garcia-Vallve HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection Nucleic Acids Res., January 11, 2008; 36(suppl_1): D524 - D527. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Diaz-Mejia, C. F. Amabile-Cuevas, I. Rosas, and V. Souza An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins Microbiology, January 1, 2008; 154(1): 94 - 102. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Becq, M. C. Gutierrez, V. Rosas-Magallanes, J. Rauzier, B. Gicquel, O. Neyrolles, and P. Deschavanne Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli Mol. Biol. Evol., August 1, 2007; 24(8): 1861 - 1871. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Ou, X. He, E. M. Harrison, B. R. Kulasekara, A. B. Thani, A. Kadioglu, S. Lory, J. C. D. Hinton, M. R. Barer, Z. Deng, et al. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands Nucleic Acids Res., July 13, 2007; 35(suppl_2): W97 - W104. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Puigbo, E. Guzman, A. Romeu, and S. Garcia-Vallve OPTIMIZER: a web server for optimizing the codon usage of DNA sequences Nucleic Acids Res., July 13, 2007; 35(suppl_2): W126 - W131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. K. Azad and J. G. Lawrence Detecting laterally transferred genes: use of entropic clustering methods and genome position Nucleic Acids Res., July 9, 2007; 35(14): 4629 - 4639. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Puigbo, S. Garcia-Vallve, and J. O. McInerney TOPD/FMTS: a new software to compare phylogenetic trees Bioinformatics, June 15, 2007; 23(12): 1556 - 1558. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. C. Miller, D. P. Keymer, A. Avelar, A. B. Boehm, and G. K. Schoolnik Detection and Transformation of Genome Segments That Differ within a Coastal Population of Vibrio cholerae Strains Appl. Envir. Microbiol., June 1, 2007; 73(11): 3695 - 3704. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Touchon and E. P. C. Rocha Causes of Insertion Sequences Abundance in Prokaryotic Genomes Mol. Biol. Evol., April 1, 2007; 24(4): 969 - 981. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Earl, R. Losick, and R. Kolter Bacillus subtilis Genome Diversity J. Bacteriol., February 1, 2007; 189(3): 1163 - 1170. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, and F. Meyer GISMO--gene identification using a support vector machine for ORF classification Nucleic Acids Res., January 28, 2007; 35(2): 540 - 549. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. H. Yoon, Y.-K. Park, S. Lee, D. Choi, T. K. Oh, C.-G. Hur, and J. F. Kim Towards pathogenomics: a web-based resource for pathogenicity islands Nucleic Acids Res., January 12, 2007; 35(suppl_1): D395 - D400. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Jin, L. Nakhleh, S. Snir, and T. Tuller Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study Mol. Biol. Evol., January 1, 2007; 24(1): 324 - 337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. S. Vernikos and J. Parkhill Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands Bioinformatics, September 15, 2006; 22(18): 2196 - 2203. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. Heizer Jr, D. W. Raiford, M. L. Raymer, T. E. Doom, R. V. Miller, and D. E. Krane Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis Mol. Biol. Evol., September 1, 2006; 23(9): 1670 - 1680. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Erauso, K. M. Stedman, H. J. G. van de Werken, W. Zillig, and J. van der Oost Two novel conjugative plasmids from a single strain of Sulfolobus Microbiology, July 1, 2006; 152(7): 1951 - 1968. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Gao and C.-T. Zhang GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W686 - W691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Rosas-Magallanes, P. Deschavanne, L. Quintana-Murci, R. Brosch, B. Gicquel, and O. Neyrolles Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis Mol. Biol. Evol., June 1, 2006; 23(6): 1129 - 1135. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Ou, L.-L. Chen, J. Lonnen, R. R. Chaudhuri, A. B. Thani, R. Smith, N. J. Garton, J. Hinton, M. Pallen, M. R. Barer, et al. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria Nucleic Acids Res., January 9, 2006; 34(1): e3 - e3. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Coombs and T. Barkay New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea Appl. Envir. Microbiol., November 1, 2005; 71(11): 7083 - 7091. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tsirigos and I. Rigoutsos A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes Nucleic Acids Res., July 8, 2005; 33(12): 3699 - 3707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. W. J. van Passel, A. C. M. Luyf, A. H. C. van Kampen, A. Bart, and A. van der Ende {delta}{rho}-Web, an online tool to assess composition similarity of individual nucleic acid sequences Bioinformatics, July 1, 2005; 21(13): 3053 - 3055. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Belda, A. Moya, and F. J. Silva Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria Mol. Biol. Evol., June 1, 2005; 22(6): 1456 - 1467. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. Gillings, M. P. Holley, H. W. Stokes, and A. J. Holmes Integrons in Xanthomonas: A source of species genome diversity PNAS, March 22, 2005; 102(12): 4419 - 4424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. V. Beste, J. Peters, T. Hooper, C. Avignone-Rossa, M. E. Bushell, and J. McFadden Compiling a Molecular Inventory for Mycobacterium bovis BCG at Two Growth Rates: Evidence for Growth Rate-Mediated Regulation of Ribosome Biosynthesis and Lipid Metabolism J. Bacteriol., March 1, 2005; 187(5): 1677 - 1684. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tsirigos and I. Rigoutsos A new computational method for the detection of horizontal gene transfer events Nucleic Acids Res., February 16, 2005; 33(3): 922 - 933. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Dufraigne, B. Fertil, S. Lespinats, A. Giron, and P. Deschavanne Detection and characterization of horizontal transfers in prokaryotes using genomic signature Nucleic Acids Res., January 13, 2005; 33(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Medrano-Soto, G. Moreno-Hagelsieb, P. Vinuesa, J. A. Christen, and J. Collado-Vides Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes Mol. Biol. Evol., October 1, 2004; 21(10): 1884 - 1894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. W. J. van Passel, A. Bart, R. J. A. Waaijer, A. C. M. Luyf, A. H. C. van Kampen, and A. van der Ende An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes Nucleic Acids Res., August 10, 2004; 32(14): e114 - e114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang, J. F. Preston III, and T. Romeo The pgaABCD Locus of Escherichia coli Promotes the Synthesis of a Polysaccharide Adhesin Required for Biofilm Formation J. Bacteriol., May 1, 2004; 186(9): 2724 - 2734. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F.-B. Guo, H.-Y. Ou, and C.-T. Zhang ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes Nucleic Acids Res., March 15, 2003; 31(6): 1780 - 1789. [Abstract] [Full Text] [PDF]
|
|