PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences

Andrzej Zielezinski; Sebastian Deorowicz; Adam Gudyś

doi:10.1093/bioinformatics/btab837

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences

Bioinformatics. 2022 Feb 7;38(5):1447-1449. doi: 10.1093/bioinformatics/btab837.

Authors

Andrzej Zielezinski¹, Sebastian Deorowicz², Adam Gudyś²

Affiliations

¹ Department of Computational Biology, Adam Mickiewicz University, Poznan 61-614, Poland.
² Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100, Poland.

Abstract

Summary: Phage-Host Interaction Search Tool (PHIST) predicts prokaryotic hosts of viruses based on exact matches between viral and host genomes. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14-20 percentage points). PHIST is also two orders of magnitude faster than alignment-based tools making it suitable for metagenomics studies.

Availability and implementation: GNU-licensed C++ code wrapped in Python API available at: https://github.com/refresh-bio/phist.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages* / genetics
Metagenome
Metagenomics
Software
Viruses* / genetics

Grants and funding

2018/31/D/NZ2/00108/National Science Centre