ATGme

ATGme optimizes coding DNA sequences to match host-specific codon usage frequencies, for example adapting human genes for expression in Escherichia coli, to improve recombinant protein expression.

Key Features:

• Identification of Rare Codons: Identifies rare and highly rare codons within input DNA sequences based on organism-specific codon usage frequencies.
• One-Click Optimization: Automatically replaces rare codons with synonymous codons preferred in the target host according to codon usage frequencies.
• Bulk Optimization by Codon-Type: Performs bulk replacements categorized by types of rare codons to broadly adjust the codon composition of a sequence.
• Individualized Custom (Codon-by-Codon) Optimization: Enables manual, codon-by-codon replacement allowing precise selection of synonymous codons for each position.

Scientific Applications:

• Recombinant Protein Expression: Optimizes coding sequences to increase protein expression in heterologous hosts such as Escherichia coli.
• Synthetic Biology and Genetic Engineering: Facilitates codon adaptation for design and construction of genetic constructs in synthetic biology workflows.
• Biopharmaceutical and Industrial Production: Supports development activities including drug development, vaccine production, and industrial enzyme synthesis by improving translational efficiency.

Methodology:

Compares input sequences to codon usage frequency databases across organisms to identify suboptimal codons and suggests synonymous replacements aligned to the target host's codon usage.