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Nucleic Acids Res. 2003 Jan 1;31(1):187-9.

HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.

Author information

  • 1Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Pl Imperial Tàrraco 1, E-43005 Tarragona, Spain. vallve@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.

PMID:
12519978
[PubMed - indexed for MEDLINE]
PMCID:
PMC165451
Free PMC Article
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