alondmnt/codon-bias

Python package of codon usage bias analysis tools

codon-bias

This package provides codon usage bias (CUB) analysis tools for genomic sequences, focusing on protein coding regions, translation efficiency and synonymous mutations. These include implementations of popular models from the past four decades of codon usage study, such as:

• Nucleotide and codon k-mer statistics (GC, GC3, CpG, etc.)
• Frequency of Optimal Codons (FOP)
• Relative Synonymous Codon Usage (RSCU)
• Codon Adaptation Index (CAI), including extensions:
  • Codon pair (and k-mers) adaptation
• Effective Number of Codons (ENC), including extensions:
  • Background correction
  • Improved estimation
  • Effective number of codon pairs (and k-mers) (ENcp)
• tRNA Adaptation Index (tAI)
• Codon Pair Bias (CPB/CPS)
• Relative Codon Bias Score (RCBS)
• Normalized Translational Efficiency (nTE)
• Directional Codon Bias Score (DCBS)
• Codon Usage Frequency Similarity (CUFS)

This package also includes tools for sequence optimization based on these codon usage models, and generators of random sequence permutations that can be used to compute empirical p-values and z-scores.

installation

pip install codon-bias

documentation

Read on Read the Docs.

cite

Diament, A. (2022). codon-bias (python package) (Version 0.3.0). https://doi.org/10.5281/zenodo.8039452

contributing

Contributions of additional models to the package are welcome! Please familiarize yourself with the existing classes, and try to conform to their style.

codon-bias's Issues

Codon or Codon Pair label for get_weights

get_weights() outputs an array of 61 codons or 3721 codonpairs. Is there a fixed order? If so, what is the order of codons/codonpairs?

This script can be used in mtDNA?

Hi Alondmnt,

Thanks very much for sharing the nice script with us.

I have a small question， this script can be used in mtDNA?

Best wishes，
Deyuan