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2016 ; 8
(5
): ä Nephropedia Template TP
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HostPhinder: A Phage Host Prediction Tool
#MMPMID27153081
Villarroel J
; Kleinheinz KA
; Jurtz VI
; Zschach H
; Lund O
; Nielsen M
; Larsen MV
Viruses
2016[May]; 8
(5
): ä PMID27153081
show ga
The 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 [2].
free
free
free
