CUSTOM: Codon Usage to Specific Tissue OptiMizer

This package provides a codon optimization tool for tissue-specific gene design. It follows a probabilistic approach with two steps:

1. Translate tissue-specific codon preferences into a pool of optimal sequences
2. Select the desired sequence based on parameters of relevance.

Dependencies

• Python >= 3.7
• pandas, numpy, RNA

Installing

1. (optional) Create a virtual environment to install the tool

2. Install CUSTOM and its requirements using pip:

pip install custom_optimizer

Basic usage

As a basic example, here is the code to optimize an eGFP protein to kidney:

# Import package
from custom import TissueOptimizer
# Start the optimizer
opt = TissueOptimizer("Kidney", n_pool=100)
# Optimize the eGFP sequence
egfp = "MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK"
opt.optimize(egfp)
# Select the top 10 sequences
best_egfp_kidney = opt.select_best(by={"MFE":"min","MFEini":"max","CAI":"max","CPB":"max","ENC":"min"},homopolymers=7, top=10)

Contact

This project has been developed at Center for Genomic Regulation.

Xavier Hernandez-Alias

Martin H. Schaefer

Luis Serrano

Schaefer laboratory

Serrano laboratory

Cite

Hernandez-Alias, X., Benisty, H., Radusky, L.G., Serrano, L. & Schaefer, M. H. (2023). Using protein-per-mRNA differences among human tissues in codon optimization. Genome Biology, 24(1):34. (https://doi.org/10.1186/s13059-023-02868-2)

License

CUSTOM is under a common GNU GENERAL PUBLIC LICENSE. Plese, check LICENSE for further information.

[2021] - Centre de Regulació Genòmica (CRG) - All Rights Reserved*