PHAST 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 IN pipelines

 (4)
2015
PMCID: 4440953
PMID: 25999573
DOI: 10.1128/genomeA.00480-15

[…] share 5 spacers in crispr 3, while lmd-9 has only 8 spacers in this locus. the genome of smq-301 also encodes two type-i restriction-modification systems. although prophage genes were detected by phast (20), no complete prophage is present., no known toxins were identified in the coding sequence of s. thermophilus smq-301 by the web server virulencefinder (21) or by comparing the protein […]

2015
PMCID: 4497714
PMID: 26158264
DOI: 10.1371/journal.pone.0130810

[…] from the ncbi database and to map the pghp-like gene in its corresponding genomic sequence. presence and map position of prophage regions were determined by analyzing each genome/contig with the phage search tool (phast) web server [42] by using the genomic gi. potential co-localization of pghp-like genes within prophage regions was manually examined. gi and map position of pghp-like genes, […]

2015
PMCID: 4497714
PMID: 26158264
DOI: 10.1371/journal.pone.0130810

[…] and to map the pghp-like gene in its corresponding genomic sequence. presence and map position of prophage regions were determined by analyzing each genome/contig with the phage search tool (phast) web server [42] by using the genomic gi. potential co-localization of pghp-like genes within prophage regions was manually examined. gi and map position of pghp-like genes, gi of genomes […]

2014
PMCID: 4230813
PMID: 25401060
DOI: 10.1186/s13568-014-0037-8

[…] (tamura et al. [2011]). phylogenetic tree was constructed using the neighbor-joining method (saitou and nei [1987])., the ten p. putida genomes were analyzed for presence of prophages using the phast (phage search tool) prophage finder database (zhou et al. [2011]). insertion sequence (is) elements in the p. putida genomes were identified using the isfinder tool (siguier et al. [2006]; […]

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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