PHASTER statistics

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Protocols

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 citations

 (132)
call_split

Complete Genome Sequences of Two Atypical Enteropathogenic Escherichia coli O145 Environmental Strains

2018
Genome Announc
PMCID: 5946043
PMID: 29748413
DOI: 10.1128/genomeA.00418-18
call_split See protocol

[…] nomes, while 578 and 457 CDSs are specific to RM14715 and RM14723, respectively. Prophages contributed largely to the strain-specific CDSs in both genomes. Among the 15 intact prophages identified by PHASTER (, ) in RM14715 (n = 7) and RM14723 (n = 8), only 2 are common. Strains RM14715 and RM14723 are classified as atypical EPEC strains since they each contain a complete locus of enterocyte effac […]

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

[…] ages that have this gene. Additionally, each prophage sequence feature represents a specific evolutionary event in the bacterial genome (Brüssow et al., ).Here, we analyzed every sequence detected by PHASTER (Arndt et al., ) as a distinct operational unit that has its own discriminative weight among Salmonella strains. Moreover, we identified prophage sequence clusters based on the similarity and […]

library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] Potential prophage sequences in the genome were identified and categorized (intact, incomplete or questionable) using the PHASTER website (http://phaster.ca/) []. Insertion sequences located within the genome were identified using the ISfinder website (https://www-is.biotoul.fr/) [] using a cutoff of 75% identity across […]

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

[…] e 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/software/figtree/; last […]

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

[…] The sequence of the Stx converting phage was extracted from the complete genome by using the PHASTER (http://phaster.ca/), the genome of Stx converting phage was reannotated using the RAST server (http://rast.nmpdr.org/), and then manually verified and corrected. Functional annotation of sele […]

library_books

Genome Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate Oxidising Bacteria

2018
Genes
PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] . phaeum strain PB (accession number CP003732), and P. lettingae strain TMO (accession number CP000812.1) were compared using the MaGe web-based platform. Prophage sequences were identified using the PHASTER web server []. Tandem duplicated genomic regions of protein coding genes were calculated on the basis of identity (≥35%), minLRap (≥0.8) and gene separation (maximum of five consecutive genes) […]

Citations

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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

 (5)
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avilella

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Web
The server was marked as down for maintenance: first time I checked was 27-Aug-2019

Ilhem Meniaï

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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