JCat

JCat optimizes codon usage of target gene sequences to match host organism preferences and improve heterologous protein expression.

Key Features:

• Rapid Adaptation Process: Automates codon adaptation by comparing target sequences to preferred codon usage profiles of prokaryotic and eukaryotic hosts without requiring manually selected reference genes.
• Avoidance of Unwanted Sites: Allows avoidance of restriction enzyme cleavage sites and Rho-independent transcription terminators during sequence adaptation.
• Graphical and Numerical Output: Generates graphical and numerical outputs including Codon Adaptation Index (CAI) values for original and adapted sequences.
• Batch Processing Capability: Processes multiple genes in FASTA format for simultaneous CAI calculation and codon adaptation.
• Integration with PRODORIC Database: Uses codon usage data integrated from the PRODORIC database to inform adaptation.

Scientific Applications:

• Heterologous expression optimization: Adapts gene sequences to host codon preferences to enhance heterologous protein production.
• Cloning-compatible sequence design: Produces sequences that avoid common restriction sites and Rho-independent terminators to facilitate molecular cloning and expression.
• Cross-species gene adaptation examples: Has been applied to adapt genes from Caenorhabditis elegans to Escherichia coli and to adapt the Pseudomonas aeruginosa exbD gene for expression in Escherichia coli.

Methodology:

Analyzes input nucleotide sequences, compares codon frequencies to the selected host codon usage (using PRODORIC codon data), computes Codon Adaptation Index (CAI), and generates optimized sequences while avoiding specified restriction enzyme cleavage sites and Rho-independent transcription terminators; supports batch processing of FASTA files.