Identification of endogenous viral elements (EVE) in host genome

Purpose

The EVE_annotation scripts is developed to identify Endogenous Viral Elements (EVE) within genomic sequences. It takes advantage of several established bioinformatics tools and custom scripts to accurately annotate and analyze potential EVEs.

Table of Contents

• Purpose
• Installation
• Dependencies
• Usage
• Directory contents
• Contributing
• License

Installation

Clone this repository to your local machine and provide necessary permissions to the scripts using the following commands:

git clone https://github.com/carolebelliardo/EVE_annotation.git
chmod +x EVE_annotation

Then, download

1. Viral proteins on the NCBI using web page downloading service <path_to_db1>
2. The complet NR database <path_to_db2> using the following command:

wget -Nc -o wgetNRfasta.log 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz'
gzip -d nr.gz
chmod 775 nr

Dependencies

The EVE Detection Tool relies on the following external tools and libraries:

• Diamond: A sequence aligner for protein and translated DNA searches ¹.
• Bedtools: A powerful toolset for genome arithmetic².
• R: A programming language for statistical computing and graphics³.
• Python 3: A programming language required for executing the provided Python scripts⁴.

The following R librairies are required:

library(data.table)
library(taxonomizr)

Ensure that these softwares are installed and accessible in your system's PATH before running the EVE annotation scripts.

Usage

cd EVE_annotation
./EVE_annotation.sh <path_to_db1> <path_to_db2> <path_to_host_fasta>

Replace <path_to_db1>, <path_to_db2>, and <path_to_host_fasta> with the paths to the required database and input files.

Directory contents

The EVE annotation directory consists of the following scripts:

* EVE_annotation.sh: The main script that coordinates the entire EVE annotation process.
* bestHitsToFasta.py: Python script to parse BLAST results for identifying best hits and returning a FASTA file.
* absolutPosi.R: R script for absolute coordinate calculations.
* Get_EVE_annotation_summary.r: R script to generate a summary of EVE lineages.
* addFamily.py: Python script to add family information to EVE annotations.

Authors

• Carole Belliardo: [email protected]
• Clément Gilbert: [email protected]

Acknowlegements

We acknowledge the people involved in generating the genome assembly data for their publications and for making the data publicly available. We also would like to acknowledge members of the ITN Insect Doctors consortium and the current members of IRBI who provided some feedback throughout the study.

Contributing

Contributions to the EVE Detection Tool are welcome! If you find any issues or have suggestions for improvements, please open an issue or submit a pull request in the GitHub repository.

License

This project is licensed under the MIT License.

References

Footnotes

1. Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59-60. DOI: 10.1038/nmeth.3176 ↩

2. Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. DOI: 10.1093/bioinformatics/btq033 ↩

3. R Core Team (2021). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/ ↩

4. Python Software Foundation. (2021). Python Language Reference, version 3.9.6. URL: https://www.python.org/ ↩