WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

SUMMARY: WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hu...

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Detalles Bibliográficos
Autores principales: Galiez, Clovis, Siebert, Matthias, Enault, François, Vincent, Jonathan, Söding, Johannes
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870724/
https://www.ncbi.nlm.nih.gov/pubmed/28957499
http://dx.doi.org/10.1093/bioinformatics/btx383
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author Galiez, Clovis
Siebert, Matthias
Enault, François
Vincent, Jonathan
Söding, Johannes
author_facet Galiez, Clovis
Siebert, Matthias
Enault, François
Vincent, Jonathan
Söding, Johannes
author_sort Galiez, Clovis
collection PubMed
description SUMMARY: WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hundreds of times faster, making it suited for metagenomics studies. AVAILABILITY AND IMPLEMENTATION: OpenMP-parallelized GPL-licensed C ++ code available at https://github.com/soedinglab/wish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-58707242018-04-05 WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs Galiez, Clovis Siebert, Matthias Enault, François Vincent, Jonathan Söding, Johannes Bioinformatics Applications Notes SUMMARY: WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hundreds of times faster, making it suited for metagenomics studies. AVAILABILITY AND IMPLEMENTATION: OpenMP-parallelized GPL-licensed C ++ code available at https://github.com/soedinglab/wish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-10-01 2017-07-13 /pmc/articles/PMC5870724/ /pubmed/28957499 http://dx.doi.org/10.1093/bioinformatics/btx383 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Galiez, Clovis
Siebert, Matthias
Enault, François
Vincent, Jonathan
Söding, Johannes
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title_full WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title_fullStr WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title_full_unstemmed WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title_short WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
title_sort wish: who is the host? predicting prokaryotic hosts from metagenomic phage contigs
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870724/
https://www.ncbi.nlm.nih.gov/pubmed/28957499
http://dx.doi.org/10.1093/bioinformatics/btx383
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