DOI: 10.5281/zenodo.18551738
title: HERVarium self-contained local distribution for local interactive exploration of human endogenous retroviruses

description: 📦 HERVarium – self-contained local distribution

This Zenodo record provides a self-contained, runnable distribution of HERVarium, an interactive Dash-based web application for exploring a genome-wide atlas of human endogenous retroviruses (HERVs).

The archive contains all files required to run HERVarium locally, including the application code, precomputed annotation assets, reference files, and a reproducible conda environment specification. Users can run the application by downloading and unpacking this archive, creating the conda environment, and launching the app — no additional data downloads or manual assembly are required.

This distribution is intended to support reproducibility, peer review, and long-term accessibility during the preprint and initial release phase.

🧬 Overview of HERVarium

HERVarium enables interactive, locus-level exploration of multiple HERV annotation layers through an embedded IGV genome browser and searchable data tables, including:





Internal HERV loci and protein-coding domain annotations, with domain class and HMM coverage summaries (GyDB / DFAM)




LTR regulatory annotations, including transcription factor binding motif (TFBM) matches




LTR structural architecture, including U3/R/U5 segmentation, PBS and PPT predictions, and promoter / polyadenylation signal annotations




Integrated genome browser (IGV) with locally served annotation tracks and optional external tracks



All datasets are precomputed and optimized for fast local interaction using Parquet, JSON, BED, and bigBed formats.

📁 What is included in this record

This Zenodo archive (tar.xz) contains:

Application





HERVarium Dash application (app.py)




Reproducible conda environment specification (environment.yml)



Precomputed annotation data





Aggregated and query-ready tables (.parquet, .json)




Metadata files describing domains, LTRs, and U3/R/U5 features



Genome and annotation tracks





Genome reference files required by the embedded IGV viewer (FASTA + index)




Locally hosted BED / bigBed tracks for:





Internal HERV regions




Protein-coding domains




LTR elements




U3/R/U5 segments




PBS / PPT




Promoter and poly(A) signal annotations




LTR TFBMs





Static web assets





Stylesheets




Icons and logos used by the web interface



The directory structure inside the archive matches the layout expected by the application, enabling immediate execution after extraction.

▶️ How to run HERVarium locally (summary)





Download and extract this archive:



tar -xvf hervarium.tar.xz
cd HERVarium






Create and activate the conda environment:



conda env create -f environment.yml
conda activate hervarium






Launch the application:



python app.py






Open a web browser at:



http://127.0.0.1:8050





The application runs as a local web server and does not require an internet connection for core functionality.

🧑‍🔬 Intended use

This record is provided to:





Enable transparent peer review during the preprint stage




Ensure long-term, citable access to the exact data and assets used by HERVarium




Allow readers to interactively explore HERV annotation layers locally




Support reproducibility of figures and analyses presented in the associated manuscript



🔗 Related resources

The datasets integrated into HERVarium are also available as standalone Zenodo records:





LTR regulatory atlas (U3–R–U5, motifs, PBS/PPT)https://doi.org/10.5281/zenodo.17602210




Internal HERV domain annotation (ORFs + HMM profiles)https://doi.org/10.5281/zenodo.16318927



The development repository for HERVarium is hosted on GitHub:





GitHub repository: https://github.com/funcgen/HERVarium



📖 Citation

If you use HERVarium or this distribution in your work, please cite:





This Zenodo record




The HERVarium GitHub repository




The associated preprint / manuscript describing the resource: 







Regulatory Features and Functional Specialization of Human Endogenous Retroviral LTRs: A Genome-Wide Annotation and Analysis via HERVarium


Tomàs Montserrat-Ayuso, Aurora Pujol, Anna Esteve-Codina

bioRxiv 2026.02.17.706328; doi: https://doi.org/10.64898/2026.02.17.706328