Virus Host Interaction Predictor (VHIP)

Introduction

VHIP is a machine-learning model that predict virus-microbe interactions (i.e., infection or non-infection) from genomic sequences of viruses and microbes of interest. It leverages virus-microbe coevolution signal that are extracted from genomic sequences. VHIP was trained on lab-verified virus-microbe pairs collected from literature and the NCBI virus database.

You can find more information about the philosophy and performance of VHIP here: https://www.biorxiv.org/content/10.1101/2023.11.03.565433v1

Installation

This python package can be installed with PyPI

pip install virushostinteractionpredictor

It is also available through conda-forge.

conda config --add channels conda-forge
conda install virushostinteractionpredictor

Once installed, you can import the vhip python module. See the example folder on how to run the tool.

Inputs

The inputs for VHIP are sequences for the viruses and hosts of interest. Each file should represent an unique virus/host species. In addition, a blastn between the virus and host sequences, and between viruses and host spacers are needed. If there are no results from the blastn, then the files can be empty.

Example

An example is included in the example folder. It includes virus and microbes sequences, how they should be organized (separate folders), and example blastn files. Make sure you are able to run VHIP on the example before applying to a new dataset.

Citation

https://www.biorxiv.org/content/10.1101/2023.11.03.565433v1