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Protocols

PhiSpy specifications

Information


Unique identifier OMICS_11703
Name PhiSpy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python, R
Computer skills Advanced
Version 2.3
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Sajia Akhter

Publication for PhiSpy

PhiSpy citations

 (26)
library_books

Expert Opinion on Three Phage Therapy Related Topics: Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains

2018
Viruses
PMCID: 5923472
PMID: 29621199
DOI: 10.3390/v10040178

[…] e. Due to the increasing importance of phage applications, entering prophage genomes in databases is necessary when bacterial genomes are analyzed. Algorithms for finding prophages are available like PhiSpy [], PHAST (http://phast.wishartlab.com) and PHASTER [] and genome annotations will shed light on prophage properties and this is getting less complicated the more sequence data are entered into […]

library_books

Insights into origin and evolution of α proteobacterial gene transfer agents

2017
Virus Evol
PMCID: 5721377
PMID: 29250433
DOI: 10.1093/ve/vex036

[…] rity between RcGTA and genuine viral genes, some of these regions may belong to prophages unrelated to RcGTA. Indeed, 261 out of the 474 regions (55%) overlap with putative prophages identified using PhiSpy () (). However, PhiSpy also classified the RcGTA as a prophage, suggesting that the predictions may include other false positives. Of 889 PhiSpy-predicted prophage regions within 255 α-proteoba […]

call_split

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

2017
Front Microbiol
PMCID: 5632650
PMID: 29046673
DOI: 10.3389/fmicb.2017.01940
call_split See protocol

[…] ing the annotations of the adjacent genes and concluded that all of them were functional.The search for mobile elements and phages in the genome of Ca. P. novymonadis was performed algorithmically in Phispy v. 2.3 (), as well as using database searches on the online web servers Phaster () and IS Finder using E-value cut-off of 10-2. […]

library_books

The CRISPR Spacer Space Is Dominated by Sequences from Species Specific Mobilomes

2017
MBio
PMCID: 5605939
PMID: 28928211
DOI: 10.1128/mBio.01397-17

[…] ed as (pro)viral. Among the 3,679 spacer-targeting intergenic regions, 2,799 were classified as (pro)viral.The results obtained with this classification procedure were compared to those obtained with PhiSpy (), a commonly used prophage finding tool (used with default parameters) for the protospacer matches identified in the 4,961 completely assembled genomes. Of the 1,240 spacer matches in complet […]

library_books

A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437

2017
Sci Rep
PMCID: 5567305
PMID: 28831124
DOI: 10.1038/s41598-017-09317-8

[…] The genomes of the selected Paraburkholderia strains were screened for the presence of prophages by using PHAST- version October 2015, Prophinder/ACLAME- version 04, October 2015 and PhiSpy [PhiSpyNov11_3.2]. PHAST and Prophinder identify prophage regions by using a database of known phage genes, sequence identification, tRNA identification (as phages often use tRNAs as target sit […]

library_books

Characterization of Sinorhizobium sp. LM21 Prophages and Virus Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

2017
Viruses
PMCID: 5537653
PMID: 28672885
DOI: 10.3390/v9070161

[…] parative genomic analyses of the sinorhizobial viruses, 14 complete Ensifer/Sinorhizobium genomes available in GenBank (as of 1 March 2017) were screened for the presence of prophages. The use of the PhiSpy tool [] indicated 46 potential prophage regions, which were afterwards verified by manual inspection (including identification of the predicted att sites). Finally, within the genomes of eight […]

Citations

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PhiSpy institution(s)
Computational Science Research Center, San Diego State University, San Diego, CA, USA; Department of Computer Science, San Diego State University, San Diego, CA, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Egypt; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
PhiSpy funding source(s)
Advances in Bioinformatics from the National Science Foundation (DBI 0850356)

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