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

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...

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Autores principales: Zielezinski, Andrzej, Deorowicz, Sebastian, Gudyś, Adam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8826084/
https://www.ncbi.nlm.nih.gov/pubmed/34904625
http://dx.doi.org/10.1093/bioinformatics/btab837
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author Zielezinski, Andrzej
Deorowicz, Sebastian
Gudyś, Adam
author_facet Zielezinski, Andrzej
Deorowicz, Sebastian
Gudyś, Adam
author_sort Zielezinski, Andrzej
collection PubMed
description 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.
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spelling pubmed-88260842022-02-09 PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences Zielezinski, Andrzej Deorowicz, Sebastian Gudyś, Adam Bioinformatics Applications Notes 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. Oxford University Press 2021-12-14 /pmc/articles/PMC8826084/ /pubmed/34904625 http://dx.doi.org/10.1093/bioinformatics/btab837 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Zielezinski, Andrzej
Deorowicz, Sebastian
Gudyś, Adam
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title_full PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title_fullStr PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title_full_unstemmed PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title_short PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
title_sort phist: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8826084/
https://www.ncbi.nlm.nih.gov/pubmed/34904625
http://dx.doi.org/10.1093/bioinformatics/btab837
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AT gudysadam phistfastandaccuratepredictionofprokaryotichostsfrommetagenomicviralsequences

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