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

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...

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Vydáno v:Bioinformatics (Oxford, England) Ročník 33; číslo 19; s. 3113 - 3114
Hlavní autoři: Galiez, Clovis, Siebert, Matthias, Enault, François, Vincent, Jonathan, Söding, Johannes
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press (OUP) 01.10.2017
Oxford University Press
Témata:
Applications Notes
Archaea - virology
Artificial Intelligence
Bacteria - virology
Bacteriology
Bacteriophages - genetics
Biodiversity and Ecology
Computer Science
Contig Mapping
Environmental Sciences
Genetics
Global Changes
Life Sciences
Machine Learning
Metagenomics - methods
Microbiology and Parasitology
Populations and Evolution
Protistology
Software
ISSN:1367-4803, 1367-4811, 1367-4811
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Shrnutí: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. OpenMP-parallelized GPL-licensed C ++ code available at https://github.com/soedinglab/wish. clovis.galiez@mpibpc.mpg.de or soeding@mpibpc.mpg.de. Supplementary data are available at Bioinformatics online.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
PMCID: PMC5870724
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btx383