extract_trna_gcn

<code>extract_trna_gcn</code> processes tRNA sequence data from GtRNADB to 
extract gene copy numbers for each tRNA type. This information is essential
for calculating tRNA availability weights used in TAI analysis.

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

extract_trna_gcn function

<dl><dt>trna_seq</dt>
<dd>A named vector or DNAStringSet of tRNA sequences, typically 
from GtRNADB. Sequence names should follow the standard format containing 
amino acid and anticodon information (e.g., "tRNA-Ala-AGC-1-1").</dd></dl>

Arguments

Extract tRNA gene copy numbers from nature tRNA sequences — extract_trna_gcn

<dl>

<dt>trna_seq</dt>
<dd>A named vector or DNAStringSet of tRNA sequences, typically 
from GtRNADB. Sequence names should follow the standard format containing 
amino acid and anticodon information (e.g., "tRNA-Ala-AGC-1-1").</dd>

</dl>

extract_trna_gcn: Extract tRNA gene copy numbers from nature tRNA sequences

Description

Usage

Value

Arguments

Examples