Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site -- Supplementary data

Devadatta Gosavi1¹, Iwona Wower², Irene K. Beckmann³, Ivo L. Hofacker^3,4, Jacek Wower², Michael T. Wolfinger^3,4, Joanna Sztuba-Solinska¹

_{¹Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL 36849, United States
²Department of Animal and Dairy Sciences, Auburn University, 209 Upchurch Hall, Auburn, AL 36849, United States
³Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
⁴Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria}

This repository contains additional resources that were used during preparation of the manuscript. These include custom software and data files.

Software: SHAPE_Trimmer

A Python script for trimming sequences bound by primers and concatenation of truncated files. To run the script properly, it must be executed in the same directory as the FASTQ files to be trimmed. Specifically, this script performs

• truncation of sequences in .fastq files for target BVDV IRES RNA zones as required for SHAPE-MaP

• concatenation of truncatated files into a common file for complete sequence coverage

• define input/infiles files (EDIT AS NEEDED for number of zones)

• name output filename (EDIT AS NEEDED)

• hybridization site lengths for respective primers for BVDV IRES RNA zones; these correspond to the length of primers; indices match infiles

• trimming and merging

Data files

The stk directory contains Stockholm files of structural multiples sequence nucleotide alignments that were used to

• compare published BVDV IRES RNA structures
• compute consensus structures

Citation

If you use data provided in this repository in your own work please link back to this site and cite the following publications - Thank you!

• Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
  Devadatta Gosavi, Iwona Wower, Irene K. Beckmann, Ivo L. Hofacker, Jacek Wower, Michael T. Wolfinger, Joanna Sztuba-Solinska
  bioRxiv 2021.05.13.444024 (2021) PDF | doi:10.1101/2021.05.13.444024