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Essential gene databases | Synthetic biology

Essential genes are genes that are considered to be ‘essential’ for the survival of an organism (Juhas et al., 2012; Acevedo-Rocha et al., 2013). The genome-wide identification of essential genes has been performed by single-gene knockout (Baba et al., 2006; de Berardinis et al., 2008), transposon mutagenesis (Liberati et al., 2006; Gallagher et al., 2007) and RNA interference (Ji et al., 2001). Source text: Wei et al., 2014.

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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.
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.
CEG / Cluster of Essential Genes
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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.
IFIM / Integrates quantitative Fitness Information for Microbial genes
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.
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