PanDaTox version: 1.0
The PanDaTox database aims at identifying genes and intergenic regions that are unclonable in E. coli, to aid in the discovery of new antibiotics and biotechnologically beneficial functional genes. It is also designed to improve the efficiency of metabolic engineering, by systematically identifying enzymes whose products are toxic to E. coli.
PanDaTox is a database of genes that are potentially toxic to bacteria. The construction of this database is based on computational methods that scan a microbial genome and detect specific genes that kill E. coli if cloned into it. These methods identify genes and intergenic regions that fail to propagate in E. coli in the process of whole genome shotgun sequencing, thus creating sequencing gaps. It has been shown that these sequencing gaps are frequently caused by toxic genes, which may have antimicrobial properties.
PanDaTox holds and presents a set of >40,000 genes that may be toxic to bacteria. These genes are the result of a computational analysis performed on ~400 microbial genomes. Users can search for toxic genes in their genome of interest; check who are the homologs of these toxic genes and whether these homologs are toxic as well; query the database using a keyword-based search for genes answering to specific user-supplied criteria; and perform a sequence-based search (blast) for genes in the database that are similar to a query gene of their choice. The toxicity information for each gene is presented in both numerical and graphical manners, and details on each gene, including its DNA sequence, protein sequence, and various links to external web sources are presented.