HostPhinder: A Phage Host Prediction Tool

Autores
Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; Nielsen, Morten; Voldby Larsen, Mette
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
he current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry.
Fil: Villarroel, Julia. Technical University of Denmark; Dinamarca
Fil: Kleinheinz, Kortine Annina. Technical University of Denmark; Dinamarca
Fil: Jurtz, Vanessa Isabell. Technical University of Denmark; Dinamarca
Fil: Zschach, Henrike. Technical University of Denmark; Dinamarca
Fil: Lund, Ole. Technical University of Denmark; Dinamarca
Fil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Voldby Larsen, Mette. Technical University of Denmark; Dinamarca
Materia
GENOME
K-MERS
HOST SPECIFICITY
PREDICTION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/104843
Acceder
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network_name_str CONICET Digital (CONICET)
spelling HostPhinder: A Phage Host Prediction ToolVillarroel, JuliaKleinheinz, Kortine AnninaJurtz, Vanessa IsabellZschach, HenrikeLund, OleNielsen, MortenVoldby Larsen, MetteGENOMEK-MERSHOST SPECIFICITYPREDICTIONhttps://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3he current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry.Fil: Villarroel, Julia. Technical University of Denmark; DinamarcaFil: Kleinheinz, Kortine Annina. Technical University of Denmark; DinamarcaFil: Jurtz, Vanessa Isabell. Technical University of Denmark; DinamarcaFil: Zschach, Henrike. Technical University of Denmark; DinamarcaFil: Lund, Ole. Technical University of Denmark; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Voldby Larsen, Mette. Technical University of Denmark; DinamarcaMultidisciplinary Digital Publishing Institute2016-05-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/104843Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; et al.; HostPhinder: A Phage Host Prediction Tool; Multidisciplinary Digital Publishing Institute; Viruses; 8; 5; 4-5-2016; 1-221999-4915CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1999-4915/8/5/116info:eu-repo/semantics/altIdentifier/doi/10.3390/v8050116info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:10:47Zoai:ri.conicet.gov.ar:11336/104843instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-10 13:10:48.085CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv HostPhinder: A Phage Host Prediction Tool
title HostPhinder: A Phage Host Prediction Tool
spellingShingle HostPhinder: A Phage Host Prediction Tool
Villarroel, Julia
GENOME
K-MERS
HOST SPECIFICITY
PREDICTION
title_short HostPhinder: A Phage Host Prediction Tool
title_full HostPhinder: A Phage Host Prediction Tool
title_fullStr HostPhinder: A Phage Host Prediction Tool
title_full_unstemmed HostPhinder: A Phage Host Prediction Tool
title_sort HostPhinder: A Phage Host Prediction Tool
dc.creator.none.fl_str_mv Villarroel, Julia
Kleinheinz, Kortine Annina
Jurtz, Vanessa Isabell
Zschach, Henrike
Lund, Ole
Nielsen, Morten
Voldby Larsen, Mette
author Villarroel, Julia
author_facet Villarroel, Julia
Kleinheinz, Kortine Annina
Jurtz, Vanessa Isabell
Zschach, Henrike
Lund, Ole
Nielsen, Morten
Voldby Larsen, Mette
author_role author
author2 Kleinheinz, Kortine Annina
Jurtz, Vanessa Isabell
Zschach, Henrike
Lund, Ole
Nielsen, Morten
Voldby Larsen, Mette
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv GENOME
K-MERS
HOST SPECIFICITY
PREDICTION
topic GENOME
K-MERS
HOST SPECIFICITY
PREDICTION
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv he current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry.
Fil: Villarroel, Julia. Technical University of Denmark; Dinamarca
Fil: Kleinheinz, Kortine Annina. Technical University of Denmark; Dinamarca
Fil: Jurtz, Vanessa Isabell. Technical University of Denmark; Dinamarca
Fil: Zschach, Henrike. Technical University of Denmark; Dinamarca
Fil: Lund, Ole. Technical University of Denmark; Dinamarca
Fil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Voldby Larsen, Mette. Technical University of Denmark; Dinamarca
description he current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry.
publishDate 2016
dc.date.none.fl_str_mv 2016-05-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/104843
Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; et al.; HostPhinder: A Phage Host Prediction Tool; Multidisciplinary Digital Publishing Institute; Viruses; 8; 5; 4-5-2016; 1-22
1999-4915
CONICET Digital
CONICET
url http://hdl.handle.net/11336/104843
identifier_str_mv Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; et al.; HostPhinder: A Phage Host Prediction Tool; Multidisciplinary Digital Publishing Institute; Viruses; 8; 5; 4-5-2016; 1-22
1999-4915
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1999-4915/8/5/116
info:eu-repo/semantics/altIdentifier/doi/10.3390/v8050116
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842980547159130112
score 12.993085

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