Essential genes are those indispensable for the survival of an organism under certain conditions. All essential genes of an organism constitute its minimal gene set, which plays a key role in the emerging field, synthetic biology. These efforts will have important practical implications in biological engineering, and can also enhance our understanding of basic biology.

There has been great advancement in gene essentiality studies in the past few years. So far, the genome-wide or large-scale gene essentiality screens have been performed in 15 genomes. However, experimental determination of essential genes is time-consuming and expensive. Therefore, theoretical (or in silico) prediction of essential genes is currently one of science’s challenges. To response to such challenges, we initiate a project to in silico predict essential genes reliably for more and more bacterial genomes. The detailed information of predicted essential genes are organized and listed in a Database of predicted Essential Genes — pDEG. In the current version of pDEG 1.0, predicted essential genes for 16 Mycoplasma genomes are included. To have a reliable and accurate prediction of essential genes, the strategy we adopted is mainly based on the homologous mapping, relying on closely related bacteria evolutionally. By using such a strategy, the size of pDEG is expected to grow step by step timely. The database pDEG 1.0 represents the first step of such project.

The database pDEG is organized with the same form as DEG. In pDEG, the detailed information of all the predicted essential genes can be obtained, including their names, function descriptions, the DNA sequences coding for them, the corresponding amino acid sequences, and their COG codes, etc. If a predicted essential gene codes for an enzyme, the database provides the EC number and the KEGG linkage describing the metabolic pathway in which the enzyme is involved. Users can search a predicted essential gene by their functions and names. Users can also browse and extract all the records in pDEG.