An Excel Macro Code for the Analysis of the Density and Distance between the Homologous microRNA-Binding Sites Volume 53- Issue 3

Travis Varnum¹, Carolyn Pool¹, Franziska Ahrend¹, Summer Stephens Weeks¹, Amrita Biswas¹, Delani Benjamin¹, Tanner Holloway¹, Janaiya Mason¹, Neelie Miller¹, Meet Chapani¹, Brenda Calderon¹, Martin Bouldo¹, Robert Kaltenbach¹, Kai Ding¹, Walter Bell³, Christopher A Boyd¹, Long Ma², Jiling Zhong², Anslee Finch, Siegfried B Harden¹ and Alexander V Kofman^1*

• ¹Department of Biological and Environmental Sciences, Troy University, USA
• ²Department of Computer Science, Troy University, AL, USA
• ³Department of Pathology, University of Alabama at Birmingham

Received: October 19, 2023; Published: November 01, 2023

*Corresponding author: Alexander V Kofman, Department of Biological & Environmental Sciences, 210-D MSCX (McCall Hall), Troy University, Troy, AL 36082, USA

DOI: 10.26717/BJSTR.2023.53.008418

Abstract PDF

We present a MACRO code (working name TW-iniRNA) to facilitate the analysis of the predicted miRNAbinding sites generated by the miRNAhrend software tools. The TW-miRNA code calculates the density of sites and the distance between the homologuos miRNA-binding sites.

Keywords: Code; MicroRNA; mRNA; Homologous

Abbreviations: miRNA: microRNA; mRNA: messenger RNA; HS: Homologous miRNA-binding sites; SNP: Single Nucleotide Polymorphism

The computer-assisted prediction of microRNA-binding sites upon the reference genomic sequences does not reckon with the well-known by now genomic variation, which is characteristic of all biological species [1]. We developed the miRNA-mRNA complementarity alignment tool NEIL [2], and the more complex package called miRNAhrend [3] (https://franziskaahrend.pythonanywhere.com/). The latter one is the online-available package for the prediction and visualization of the miRNA-binding sites in any RNA sequence with their following verification by the complementarity alignment. It also allows us to identify the HS [4]. The designed TW-miRNA code (Supplementary Data) uses the outputs generated by miRNAhrend to assess the density of the HS within the selected mRNA fragments and the distance between the HS. HS are shown to act synergistically. However, it depends on the distance between HS [5], whereas overlapping HS may be considered as useless. The presence of the HS may potentially rescue the miRNA potency if one of the HS is disrupted by the SNP [4]. The proposed TW-miRNA code significantly expands the functionality of the miRNAhrend package tools.

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