get_gc3s

Calculate GC content at synonymous 3rd codon positions.

A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.

Hong Zhang

cubar

Codon Usage Bias Analysis

Mengyue Liu

Bu Zi

get_gc3s function

<dl><dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_codons()</code>.</dd>
<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or <code>create_codon_table</code>.</dd>
<dt>level</dt>
<dd>"subfam" (default) or "amino_acid". For which level to determine 
GC content at synonymous 3rd codon positions.</dd></dl>

Arguments

GC contents at synonymous 3rd codon positions — get_gc3s

<dl>

<dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_codons()</code>.</dd>


<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or <code>create_codon_table</code>.</dd>


<dt>level</dt>
<dd>"subfam" (default) or "amino_acid". For which level to determine 
GC content at synonymous 3rd codon positions.</dd>

</dl>

get_gc3s: GC contents at synonymous 3rd codon positions

Description

Usage

Value

Arguments

References

Examples