TOOLS.md

Computational Tools for Host Prediction

Here are some publications and tools that describe how to predict virus host interactions or tools that could be used to do so.

Overviews of phage host interactions

• Phage-Host Interaction: an Ecological Perspective

Overview of Computational Predictions

The paper Computational approaches to predict bacteriophage–host relationships by Rob, Kate, Karoline, Jeroen, and Bas describes different approaches that could be used to calculate phage/host relationships. Not all work well, but most work.

A review of An Integrative Approach to Virus–Host Protein–Protein Interactions

Computational prediction of inter-species relationships through omics data analysis and machine learning

Computational Prediction of Host-Pathogen Interactions Through Omics Data Analysis and Machine Learning

Phage hunters: Computational strategies for finding phages in large-scale ‘omics datasets

Approaches to predict phage hosts

• Viral host prediction with Deep Learning
• Identifying viruses from metagenomic data by deep learning
• PHISDetector: a web tool to detect diverse in silico phage-host interaction signals
• Structure-based prediction of host–pathogen protein interactions
• HostPhinder: A Phage Host Prediction Tool
• Linking Virus Genomes with Host Taxonomy
• A network-based integrated framework for predicting virus-host interactions
• Prediction of virus-host infectious association by supervised learning methods
• Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus and paper
• VirHostMatcher and paper

Identifying phage sequences in metagenomes

• PhaMers identifies novel bacteriophage sequences from thermophilic hot springs
• MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
• WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
• VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
• ViraMiner: Deep Learning on Raw DNA Sequences for Identifying Viral Genomes in Human Samples
• VirSorter: mining viral signal from microbial genomic data
• Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
• MetaVir and paper

Viral Tagging

• Defining the human gut host–phage network through single-cell viral tagging
• Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
• Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

Predicting Environments

• Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

Prophage Finding

You should start with these two classics: Prophages and bacterial genomics: what have we learned so far? and Prophage Genomics

• PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies and paper
• Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
• PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
  • PHAST: A Fast Phage Search Tool
  • PHASTER: a better, faster version of the PHAST phage search tool
• Prophage Hunter: an integrative hunting tool for active prophages
• ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database
• PhageWeb and paper Note: this appears to not be available any longer, although there is this API
• Phigaro and paper

Other tools and approaches

Classifying Sequences

• Classifying the Unclassified: A Phage Classification Method

Finding ends

• PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data and paper

Databases

• VOGDB
• pVOG and paper
• Virus-Host DB

CRISPr Finding

• CRISPRdigger
• CRISPRCasFinder
  • CRISPRfinder is the old version of CRISPRCasFinder and paper
  • CRISPRdb is the related spacer database
• PILER-CR
• CRISPR recognition tool (CRT)
• CRISPI is another database
• CRISPRDirection and paper
• CRISPRmap and paper
• CRISPRTarget
• CRISPRViz and paper
• CRISPRStudio
• metaCRAST and paper
• metaCRISPR and paper
• crass (but not the real crAss) and paper