Welcome to CodonU’s documentation!

Introduction

CodonU is an integrated package for Codon Usage Analysis. This is written by Souradipto Choudhuri in 2023 and was his final year project in Biotechnology major. This is only the documentation of the project.

Please find the examples in the git repo of the project if you want one.

Contents:

Installation

pip install CodonU

References

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    1. Fuglsang, “The ‘effective number of codons’ revisited,” Biochemical and Biophysical Research Communications, vol. 317, no. 3, pp. 957–964, May 2004, doi: 10.1016/j.bbrc.2004.03.138.

      1. Sharp and W.-H. Li, “The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications,” Nucleic Acids Research, vol. 15, no. 3, pp. 1281–1295, 1987, doi: 10.1093/nar/15.3.1281.

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      1. Lobry and C. Gautier, “Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes,” Nucleic Acids Research, vol. 22, no. 15, pp. 3174–3180, Aug. 1994, doi: 10.1093/nar/22.15.3174.

      1. Lobry, Multivariate Analyses of Codon Usage Biases. ISTE Press - Elsevier, 2018. doi: 10.1016/C2018-0-02165-9.

    1. Sievers and D. G. Higgins, “Clustal Omega for making accurate alignments of many protein sequences,” Protein Science, vol. 27, no. 1, pp. 135–145, Jan. 2018, doi: 10.1002/pro.3290.

      1. Larkin et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, Nov. 2007, doi: 10.1093/bioinformatics/btm404.

  • Anwar et al., “gtAI: an improved species-specific tRNA adaptation index using the genetic algorithm”, Frontiers in Molecular Biosciences, vol. 10, Jul. 2023, doi: 10.3389/fmolb.2023.1218518.

Indices and tables