PhiSpy protocols

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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

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Maintainer


  • person_outline Sajia Akhter <>

Publication for PhiSpy

PhiSpy in pipelines

 (2)
2014
PMCID: 4141962
PMID: 25096633
DOI: 10.1186/1471-2164-15-654

[…] of protein families identified with cd-hit [], genome-wide snps [], functions and subsystems annotated by rast (rapid annotations using subsystems technology []) and phages identified by using phispy [] and homology searches (see methods). monotonous variables were removed and variables with redundant, highly correlating profiles were merged, yielding a total of 25,305 informative, […]

2013
PMCID: 3861447
PMID: 24349412
DOI: 10.1371/journal.pone.0082985

[…] host-associated plants and animals () stored in the database at the time of writing (search date 19/09/13). the img/m-hmp server can be found at: http://img.jgi.doe.gov/cgi-bin/imgm_hmp/main.cgi. phispy [] was used to identify putative prophage genes and the boundaries of the putative prophage region on smg 25. , the scaffolds on which an stla homologue was identified were subjected to blastx […]


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PhiSpy in publications

 (22)
PMCID: 5721377
PMID: 29250433
DOI: 10.1093/ve/vex036

[…] rcgta homologs, it was designated as a large cluster (lc). the remaining regions were labeled as small clusters (scs)., prophage-like regions in 255 α-proteobacterial genomes were detected using phispy v. 2.3 () with ‘−n=5’ (at least five consecutive prophage genes), ‘−w=30’ (a window size of 30 orfs), and ‘−t  =  0’ (generic test set) settings. an rcgta-like region was classified […]

PMCID: 5632650
PMID: 29046673
DOI: 10.3389/fmicb.2017.01940

[…] 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., files with the genome sequences and corresponding annotations […]

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

[…] 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 […]

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

[…] strains bs455, bifas53, j1u5 and psjn, for the presence of putative prophage-like (pp) elements (table ). for this, we used the phage identification programs phast, prophinder/aclame and phispy. by applying the criteria (see material and methods), we identified a total of 209 pp regions across the eight paraburkholderia genomes. following curation, 127 of the regions remained […]

PMCID: 5537653
PMID: 28672885
DOI: 10.3390/v9070161

[…] version 3.0 software (roche, basel, switzerland)., the lm21 draft genome was automatically annotated using rast server [,]. the prophage sequences within the draft genome were identified using phispy [] and manual inspection. then, the predicted prophage sequences were manually annotated using clone manager (sci-ed8) and artemis software []. similarity searches were performed using […]


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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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