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Protocols

PHAST specifications

Information


Unique identifier OMICS_00180
Name PHAST
Alternative name PHAge Search Tool
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline David Wishart

Publication for PHAge Search Tool

PHAST citations

 (493)
library_books

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

2018
Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] the number of contigs, size of the largest contig, number of bases in the assembly, and NG50 (data not shown). Prophage sequences within the assembled contigs of each genome were identified with the PHAge Search Tool Enhanced Release (PHASTER; Zhou et al., ; Arndt et al., ). All contigs <2 Kb were discarded before submitting the assembly to PHASTER, as PHASTER processes only contigs of length >= […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] SNPs in repetitive regions and phage sequences, the reference sequence K. pneumoniae KPNIH30 (NZ_CP009872.1) was analysed using the repeat analysis tool in Kodon (Applied Maths) version 3.62 and the phage search tool PHASTER []. Additionally, SNPs in regions of annotated phages and transposases were rejected (not shown). Trees were illustrated using FigTree v1.4.3. (http://tree.bio.ed.ac.uk/softw […]

library_books

Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain Specific Viability Quantitative PCR Method

2018
Appl Environ Microbiol
PMCID: 5930365
PMID: 29523544
DOI: 10.1128/AEM.00107-18

[…] the fragment identified by RAPD-PCR showed similarity with a prophage, raw data of sequenced L. plantarum PM411 genome were used for prophage region search and annotation using a phage finding tool (PHAge Search Tool [PHAST] []). The corresponding putative phage sequence was deposited in the GenBank database (accession number MG788324). The RAPD sequence was located in the putative prophage of L. […]

call_split

Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

2018
Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] ed to generate one circular genome without gaps by using SMRT Analysis 2.3.0. The protein-coding sequences (CDSs), tRNAs and rRNAs were predicted using GeneMarkS. The prophages were predicated by the PHAge Search Tool (PHAST). The virulence factors were predicted through the BLAST tool of NCBI and by using the virulence factor database (VFDB; http://www.mgc.ac.cn/). […]

call_split

Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrociénegas, Coahuila, Mexico

2018
Genome Announc
PMCID: 5920177
PMID: 29700165
DOI: 10.1128/genomeA.00364-18
call_split See protocol

[…] ilus 150a. Twelve genes related to the bacteriocin stress response and one conferring tolerance to colicin E2 were annotated in both strains. Both strains harbored prophage sequences, as indicated by PHAST (). B. pumilus 145 contained four intact prophage regions in the chromosome and the Bacillus phage EZ-2018a, whereas B. pumilus 150a harbored two intact prophage regions in its chromosome. A gen […]

call_split

Draft Genome Sequence of Multidrug Resistant Escherichia coli NIVEDI P44, Isolated from a Chicken Fecal Sample in Northeast India

2018
Genome Announc
PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18
call_split See protocol

[…] LST) 746 (ST746). Plasmid Finder and PLACNET (, ) detected three plasmid sequences, viz., IncN, ColpVC, and p0111 (IncHI1). Of these, p0111 harbored the tet(A) gene (encodes tetracycline resistance). PHAST analysis () detected 3 intact phages totaling 117.9 kb, which accounts for 2.46% of the total genome.Analysis by ResFinder version 2.1 (), ARDB (), and CARD () revealed the presence of the multi […]

Citations

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PHAST institution(s)
Department of Biological Sciences, Edmonton, AB, Canada; Department of Computing Science, University of Alberta, Edmonton, AB, Canada; National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada
PHAST funding source(s)
Supported by the Canadian Institutes of Health Research (CIHR) and Genome Alberta (a division of Genome Canada).

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