SRNA (Smart Rapid Nucleotide Analysis) and RMSE (RefSeq Multigene Sequence Extractor) Web Tools for Assessing Nucleotide Composition Volume 63- Issue 4

Shubh R Nahar^1,3#, Mostafizur Rahman^1#, Syeda Saberin Jahan^2,3, Giulianna Rivero⁴, Valeri Drozhenko³, Walter C Bell⁵, Kai Ding⁶, Long Ma¹, Bill Zhong¹ and Alexander Kofman^3,7*

• ¹Department of Computer Science, Troy University, AL, USA
• ²Jalalabad Ragib-Rabeya Medical College and Hospital, Bangladesh
• ³The Filatov Institute of Eye Diseases and Tissue Therapy, the National Academy of Medical Sciences, Ukraine
• ⁴Department of Biological and Environmental Sciences, Troy University, USA
• ⁵Department of Pathology, Heersink School of Medicine, The University of Alabama at Birmingham, AL, USA
• ⁶John Hopkins University Medical School, AL, USA
• ⁷University of West Alabama, AL, USA
• ^#Both authors contributed equally to this work

Received: October 03, 2025; Published: October 16, 2025

*Corresponding author: Alexander Kofman, Human Biology Variations Computational Genomics Research, The Filatov Institute of Eye Diseases and Tissue Therapy, the National Academy of Medical Sciences, Ukraine, University of West Alabama, AL, USA

DOI: 10.26717/BJSTR.2025.63.009915

Abstract PDF

We present SRNA and RMSE user-friendly web tools for retrieving and analyzing the nucleotide composition of whole and fragmented nucleic acid sequences.

Keywords: Nucleotide; mRNA; Codon

Abbreviations: mRNA: Messenger RNA; UTR: Untranslated Region

The growing number of reports indicates that codon usage bias and nucleotide composition are crucial regulatory factors that influence gene expression at various levels. These factors can affect the concentration of nuclear mRNA [1] and its stability [2,3], alter the expression of heterologous genes in bacteria, plants, yeast, mammalian cells, and transgenic animals [4], and impact the formation of Z-DNA and Z-RNA, among other effects [5,6].

SRNA 1.0 (SRNA · Streamlit) and RMSE 1.0 (NCBI RefSeq Multi- Gene Extractor · Streamlit) are user-friendly web tools that enable the retrieval of nucleotide sequences and calculation of their nucleotide composition, including G-C%, A-T%, and Z-DNA propensity by batch analysis (up to 1000 sequences). Furthermore, to assess the variations in nucleotide composition across different parts of the gene, the SRNA tool can split the original sequence into fragments of 50, 100, 200, and 400 bases.

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