CUSTOM Server

The Codon Usage to Specific Tissue OptiMizer (CUSTOM) provides a codon optimization tool for tissue-specific gene design.

This web server provides a graphical frontend to the original Python package. Please check the documentation for more advanced features.

For a description of the method, refer to the original manuscript: Hernandez-Alias et al. (2023).

New Job

Select the target tissue:

Insert an amino acid or DNA sequence:

Algorithm parameters

Number of iterations to generate a pool of optimized sequences:
10 1000

Select the best sequences based on:

Maximum Codon Adaptation Index (CAI)

Maximum Codon Pair Bias (CPB)

Minimum Effective Number of Codons (ENC)

Minimum Minimum Free Energy (MFE) after the first 40 nt

Maximum MFE at the first 40 nt

Target GC content:

Exclude nucleotide homopolymers equal or larger than:

Exclude specific motifs:

Serrano Lab
Schaefer Lab