Horizontal Gene Transfer Database (HGT-DB)

Evolutionary Genomics Group. Biochemistry and Biotechnology Department.
Universitat Rovira i Virgili (URV). Tarragona. Spain.

How to cite the HGT-DB

A new version of the HGT-DB has been created at http://genomes.urv.es/HGT-DB/



Welcome to the Horizontal Gene Transfer Database (HGT-DB). The 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 includes the analysis of 94 bacterial and archaeal complete genomes, including multiple chromosomes and strains, when available. Other complete genomes will be added progressively. The HGT-DB is organized by genome i.e. every prokaryotic genome that has been completely sequenced forms a new entry. Click here to see the organization of the database. The database is described in the article "S. Garcia-Vallve, E. Guzman, MA. Montero and A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Research 31(1):187-189".

The procedure used is described in the article "S. Garcia-Vallve, A. Romeu and J. Palau. 2000. Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes. Genome Research 10(11):1719-1725".  The procedure is based, basically, on the G+C contents, codon usages, gene positions and amino acid contents of all the genes and derived protein sequences for each organism. All the statistical parameters used in this study are accessible for all the genes, and we strongly recommend to use it. You can access by organism or by the search engine. Use these results with caution. Not all the acquired genes have anomalous codon usage or G+C content, and other forces may be responsible for the codon usage or G+C content heterogeneity of a genome. A more conclusive proposal for a gene to be considered as being acquired by HGT usually needs an individualized study that includes orthologous analysis and confirmation of an inappropriate positioning in a phylogenetic tree.

Choose the organism:
  
The organisms included are:

Bacteria:


Archaea:


This database is maintained by Dr. S. Garcia-Vallvé. Last update: July 2002.   News and previous releases

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How to cite us:

We are working hard at maintaining this server for the scientific community. If you found this server useful for your research we would appreciate if you cite the HGT-database. Mention our NAR manuscript and this server name and URL:

Garcia-Vallve et al. (2003) Horizontal gene transfer database (HGT-DB) at URL: http://www.fut.es/~debb/HGT/

S. Garcia-Vallve, E. Guzman, MA. Montero and A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Research 31:187-189.


Others web servers maintained by our group:

BIOCHEMISTRY & BIOTECHNOLOGY DEPARTMENT

This Database has been financied by:

               
(Ref. BIO2003-07672)                     (Ref. BIO 04)