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Phage_Finder specifications


Unique identifier OMICS_11701
Name Phage_Finder
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
NCBI BLASTALL, WUBLAST, HMMSEARCH, tRNAscan-SE, Aragorn, FASTA33, MUMMER, Math::Round, PERL::PHAGE::Phage_subs, Getopt::Std, XGRAPH
Maintained Yes


No version available



  • person_outline Derrick E. Fouts

Publication for Phage_Finder

Phage_Finder citations


Exploring the Genomic Traits of Non toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

Front Microbiol
PMCID: 5809470
PMID: 29472910
DOI: 10.3389/fmicb.2018.00161

[…] used to screen putative virulence factors using selected databases of Escherichia coli, Enterococcus, and Streptococcus aureus. Prophage-like elements were identified by running bacterial genomes in Phage_Finder v2.1 () and PHAST (). […]


Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY Q

Front Microbiol
PMCID: 5674928
PMID: 29163390
DOI: 10.3389/fmicb.2017.02085

[…] inder (Varani et al., ) and then manually curated with focuses on intactness, terminal inverse repeats (IRs) and flanking direct repeats (DRs). Prophages were predicted with PHAST (Zhou et al., ) and Phage_Finder (Fouts, ), and cognate boundaries were systemically checked. The 16S rRNA and proteome phylogenetics tree was inferred by PhyML (Guindon et al., ) and CVtree (Xu and Hao, ) with the maxim […]


The chromosomal organization of horizontal gene transfer in bacteria

Nat Commun
PMCID: 5635113
PMID: 29018197
DOI: 10.1038/s41467-017-00808-w

[…] Temperate phages integrated in the bacterial chromosome (prophages) were identified using Phage Finder v4.6 (stringent option). Prophages with > 25% of the predicted genes belonging to ISs, and partially degraded prophages (shorter than 30 kb) were removed. Integrons were identified using […]


A widespread family of polymorphic toxins encoded by temperate phages

BMC Biol
PMCID: 5576092
PMID: 28851366
DOI: 10.1186/s12915-017-0415-1

[…] ate phages). The general characteristics and the result of lifestyle prediction for each phage are listed in Additional file : Table S1.Prophages were detected in bacterial chromosomes as in [] using Phage Finder v4.6 []. The elements larger than 18 kb were considered as prophages. The smaller elements identified by Phage Finder may be prophage remnants or erroneous assignments. Thus, we identifie […]


Expanding landscapes of the diversified mcr 1 bearing plasmid reservoirs

PMCID: 5500976
PMID: 28683827
DOI: 10.1186/s40168-017-0288-0
call_split See protocol

[…] epeats (DRs). ISCR elements were also identified ( Prophages were predicted with PHAST [] and Phage_Finder []. Resistance genes were in silico identified with ARDB [], CARD [], and ResFinder []. […]


Genome wide analysis of a avirulent and reveal the strain induces pro tective immunity against challenge with virulent Streptococcus suis Serotype 2

BMC Microbiol
PMCID: 5351164
PMID: 28292261
DOI: 10.1186/s12866-017-0971-0

[…] he S.suis serotype 2 strains, the devil of account genes from phages, but no useful information was acquired to hint that contain prophage in these strain chromosome with prophage prediction software phage finder [], except a few transposases local in these fragment upstream or downstream such as on sequence of 05HAS68 chromosome site at bases 630703 to 788878 (IS111A), bases 868905 to 920358 (IS2 […]


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Phage_Finder institution(s)
The Institute for Genomic research, Medical Center Drive, Chinakville, MD, USA

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