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Codon bias in protein-coding genes

Goals:

Does my protein coding data display gene-wide or site-specific codon biases ?

Why:

Strong codon biases are thought to be due to translational selection, and often found in highly expressed genes. Synthetic modification of codon bias was shown capable of causing multiple-fold increases of in expression.

Input data:

1. A set of protein-coding sequences in fasta format or other standard format.
(2.) Corresponding gene expression, mRNA transcript and protein abundance data can be provided.

Pipeline:

1. Compute CAI
2. Compute effective number of codons
3. Compute TPI
4. Compute CG and CG3
5. Correlate abundances with codon bias measures (if applies)
6. Detect significant deviations from background expectation

Deliverables:

List of corresponding codon bias measures and results of statistical correlations and significance tests.
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