Essential genes are genes that are considered to be ‘essential’ for the survival of an organism. The genome-wide identification of essential genes has been performed by single-gene knockout, transposon mutagenesis and RNA interference.
Its main purpose is to enhance our understanding of the essentiality of genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development.
A publicly and freely available platform that addresses the increasing need of next generation sequencing data analysis in the Drosophila research community. FlyVar is composed of three parts. First, a database that contains 5.94 million DNA polymorphisms found in Drosophila melanogaster derived from whole genome shotgun sequencing of 612 genomes of D. melanogaster. In addition, a list of 1,094 dispensable genes has been identified. Second, a graphical user interface (GUI) has been implemented to allow easy and flexible queries of the database. Third, a set of interactive online tools enables filtering and annotation of genomic sequences obtained from individual D. melanogaster strains to identify candidate mutations. FlyVar permits the analysis of next generation sequencing data without the need of extensive computational training or resources.
Provides integrated microbial fitness data from both experiments and computational simulations. The integrated fitness data in IFIM originate from experiments of single-gene deletion mutants, libraries of transposon integrations and computational simulations using Geptop. IFIM overlaps with the existing DEG, OGEE and CEG databases, but differs from them in that it provides quantitative fitness values for the genes.
Essential genes are those indispensable for the survival of an organism, and therefore are considered a foundation of life. DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.
Contains clusters of orthologous essential genes. Based on the size of a cluster, users can easily decide whether an essential gene is conserved in multiple bacterial species or is species-specific. CEG contains the similarity value of every essential gene cluster against human proteins or genes. Properties contained in the CEG database, such as cluster size, and the similarity of essential gene clusters against human proteins or genes, are very important for evolutionary research and drug design.
A synthetic biology database of experimentally genetic validated logic gates. LGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.