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PHERI—Phage Host ExploRation Pipeline
Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly lik...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10305434/ https://www.ncbi.nlm.nih.gov/pubmed/37374901 http://dx.doi.org/10.3390/microorganisms11061398 |
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author | Baláž, Andrej Kajsik, Michal Budiš, Jaroslav Szemes, Tomáš Turňa, Ján |
author_facet | Baláž, Andrej Kajsik, Michal Budiš, Jaroslav Szemes, Tomáš Turňa, Ján |
author_sort | Baláž, Andrej |
collection | PubMed |
description | Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection. |
format | Online Article Text |
id | pubmed-10305434 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-103054342023-06-29 PHERI—Phage Host ExploRation Pipeline Baláž, Andrej Kajsik, Michal Budiš, Jaroslav Szemes, Tomáš Turňa, Ján Microorganisms Article Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection. MDPI 2023-05-26 /pmc/articles/PMC10305434/ /pubmed/37374901 http://dx.doi.org/10.3390/microorganisms11061398 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Baláž, Andrej Kajsik, Michal Budiš, Jaroslav Szemes, Tomáš Turňa, Ján PHERI—Phage Host ExploRation Pipeline |
title | PHERI—Phage Host ExploRation Pipeline |
title_full | PHERI—Phage Host ExploRation Pipeline |
title_fullStr | PHERI—Phage Host ExploRation Pipeline |
title_full_unstemmed | PHERI—Phage Host ExploRation Pipeline |
title_short | PHERI—Phage Host ExploRation Pipeline |
title_sort | pheri—phage host exploration pipeline |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10305434/ https://www.ncbi.nlm.nih.gov/pubmed/37374901 http://dx.doi.org/10.3390/microorganisms11061398 |
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