PHASTER pipeline

PHASTER specifications

Information


Unique identifier OMICS_11700
Name PHASTER
Alternative name PHAge Search Tool - Enhanced Release
Interface Web user interface
Restrictions to use None
Input data Nucleotide sequence data or an annotated genome data
Input format FASTA or GenBank
Programming languages Javascript
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David Wishart <>

Publication for PHAge Search Tool - Enhanced Release

PHASTER IN pipelines

 (6)
2018
PMCID: 5794082
PMID: 29389941
DOI: 10.1371/journal.pone.0191362

[…] to none of the bovine epec strains and only 2 of 6 human ehec strains., †number of prophage sequences were determined from whole genome sequences of strains using phage search tool enhanced release (phaster) [31, 32]., only intact and questionable prophage counts based on phaster scores of >90 and 70–90, respectively, are shown., a maximum likelihood phylogenetic tree, based on core genome […]

2018
PMCID: 5807335
PMID: 29459888
DOI: 10.3389/fcimb.2018.00020

[…] the coverage of these regions was 2.4–4.7 times below the genome coverage while, they were barely detectable in the samples processed by illumina sequencing (image s1). the phages identified by phaster (arndt et al., 2016) are the following: in contig_1 and contig_2, two intact prophages lp-030-3 (genbank accession number nc_024384.1) and vb_lmos_293 (genbank accession number nc_028929.1), […]

2018
PMCID: 5845691
PMID: 29559964
DOI: 10.3389/fmicb.2018.00383

[…] searched using the card database version 1.1.2 (comprehensive antibiotic resistance database; mcarthur et al., 2013) included in the microscope platform. prophage sequences were identified using the phaster tool (arndt et al., 2016) and manually confirmed by eliminating false positive “incomplete prophages” (e.g., transposons). in addition, clustered regularly interspaced short palindromic […]

2017
PMCID: 5216340
PMID: 28057934
DOI: 10.1038/srep40206

[…] from the same strains, then we selected the reference strains as represent according to the primary paper for our analyses (detail in supplemental table s2)3031. the prophages were identified using phaster32. we removed prophages with a large number of insertion sequences (is; >25% of the predicted orfs). microsoft excel was used for all the statistical analysis., crispr array […]

2017
PMCID: 5604178
PMID: 29617829
DOI: 10.1093/gbe/evx165

[…] 2012) (supplementary table s1, supplementary material online). a genetic environment of cry1 was visualized with easyfig tool (sullivan etal. 2011). in addition, isfinder (siguier etal. 2006) and phaster (arndt etal. 2016) website tools were used in order to identify mobile elements and prophage regions, respectively. dna sequence alignment and analysis were performed with clc genomic […]

PHASTER institution(s)
Department of Computing Science, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; National Institute for Nanotechnology, Edmonton, Canada
PHASTER funding source(s)
Canadian Institutes of Health Research (CIHR); Genome Alberta, a division of Genome Canada

PHASTER reviews

 (3)
star_border star_border star_border star_border star_border
star star star star star

Ilhem Meniaï

star_border star_border star_border star_border star_border
star star star star star
Web
Easy to use and rather fast depending on the amount of peiple on the server. Nice to have a summary and a more detailed output. Overall i like the fact that it takes large input files

Juraj Bugala

star_border star_border star_border star_border star_border
star star star star star
Web
easy to use, can work with accession numbers, nice result charts and graphic, you can download the result
BUT
in 1 case there was 9 prophage regions in summary mode and 30 phages in genome viewer mode for the same sequence. cant figure out why