Evolutionary Genomics Group Biochemistry and Biotechnology Department
Universitat Rovira i Virgili (URV). Tarragona. Spain.
Welcome to the Horizontal Gene Transfer Database (HGT-DB).
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 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.
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.
Our methodology used to predict the acquired genes is very strict in order to reduce the false positives.
This means however that there are an important number of false negatives
(See the following table
from Azad and Lawrence NAR 2007 doi:10.1093/nar/gkm204).
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.
How to use the HGT-DB ?
You can access the database by organism or by the search engine.
Select one or more genomes and click the "See the organisms included in the DB" button to see the list of all genomes available in the database.
Two search engines are available: the first one allows searching by organism, gene name, function, ... The second one allows metabollic searches.
How to cite the HGT-DB:
Garcia-Vallve et al. (2003) Horizontal gene transfer database (HGT-DB) at URL: http://genomes.urv.es/HGT-DB/
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.
