Python Codon Tables

Provides codon usage tables as dictionaries, for Python.

Tables for the following organisms are provided with the package (other tables can be downloaded using a TaxID):

• B. subtilis
• C. elegans
• D. melanogaster
• E. coli
• G. gallus
• H. sapiens
• M. musculus
• M. musculus domesticus
• S. cerevisiae

All tables are from kazusa.or.jp (codon usages were computed using NCBI sequence data). The original publication:

Codon usage tabulated from the international DNA sequence databases:
status for the year 2000.
Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.

Usage

import python_codon_tables as pct

# PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES
print ('Available tables:', pct.available_codon_tables_names)

# LOAD ONE TABLE BY NAME
table = pct.get_codons_table("b_subtilis_1423")
print (table['T']['ACA'])  # returns 0.4
print (table['*']['TAA'])  # returns 0.61

# LOAD ONE TABLE BY TAXID (it will get it from the internet if it is not
# in the builtin tables)
table = pct.get_codons_table(1423)
print (table['T']['ACA'])  # returns 0.4
print (table['*']['TAA'])  # returns 0.61

# LOAD ALL BUIL-IN TABLES AT ONCE
codons_tables = pct.get_all_available_codons_tables()
print (codons_tables['c_elegans_6239']['L']['CTA'])  # returns 0.09

• Notice that by default the tables use nucleotide T instead of U. Using get_codons_table('e_coli', replace_U_by_T=False) will leave Us as Us.
• In get_codons_table you can also provide a "shorthand" notation b_subtilis, which will be automatically extended to b_subtilis_1423 as it appears so in the built-in table (use this feature at your own risks!)

The package can also use codon usage data from a CSV file in the form:

` amino_acid,codon,relative_frequency *,UAA,0.64 *,UAG,0.07 *,UGA,0.29 A,GCA,0.21 A,GCC,0.27 K,AAA,0.76 K,AAG,0.24 etc. `

Contribute

This project was started at the Edinburgh Genome Foundry by Zulko and is released on Github under the CC0 (Public Domain) license (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.

Installation

via pip:

pip install python_codon_tables

Manual:

python setup.py install

More biology software

This library is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.