Deciphering the Nucleotide Distribution Dynamics of rDNA Internal Transcribed Spacer 1 in Fish Species Rita rita Using R Programming

The internal transcribed spacer region 1 (ITS1) of Rita rita was explored using R programming language with an approach to better interpret its secondary structure in terms of its sequence and structural attributes. It has shown a multi-helical secondary structure composed of loops and self-complementary helical regions. A series of functions from tidyverse core packages and bioseq package in RStudio were used to extract the information from ITS1. The distribution frequency of nucleotides and base pairs were traced on the constituent helices of secondary structure. Moreover, the self-complementary sequence motifs were also extracted and tabulated. Additionally, statistical computing and data visualization using R programming approach has made it easier to represent the sequence data graphically using ggplot by providing direct functions which in turns provided a very effective preliminary characterization of nucleotide composition and dynamics of this non-coding ITS1 region.