EcoliGD

EcoliGD performs comprehensive in silico genome design and recoding of Escherichia coli K-12 substr. MG1655 to support synthetic biology and functional genomics investigations.

Key Features:

• Genome modification operations: In silico insertion, exchange, deletion, and codon replacement on the Escherichia coli K-12 substr. MG1655 genome.
• Whole-genome recoding: Support for recoding the entire Escherichia coli genome to explore altered genetic codes and sequence variants.
• Experimentally verified genomic segments: A curated collection of large genomic segments experimentally deleted from E. coli available for incorporation into designs.
• Gene functional annotations: Detailed functional information and annotations for E. coli genes to inform design and interpretation.

Scientific Applications:

• Synthetic genome design: Design and evaluation of engineered E. coli genomes and large-scale genome reductions.
• Functional genomics: Investigation of gene function and gene–phenotype relationships in E. coli K-12 substr. MG1655.
• Metabolic engineering and strain optimization: Design of genomic modifications to alter metabolic pathways and cellular processes for desired traits.
• Genetic code and recoding studies: Exploration of recoding strategies and their effects on genetic diversity and function.

Methodology:

Performs in silico insertion, exchange, deletion, codon replacement, and whole-genome recoding on the Escherichia coli K-12 substr. MG1655 genome using curated gene functional annotations and a collection of experimentally verified deleted genomic segments.