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Prophage Finder specifications

Information


Unique identifier OMICS_11699
Name Prophage Finder
Interface Web user interface
Restrictions to use None
Input data DNA sequences ranging from 5 kb to 10 Mb
Input format FASTA
Programming languages Perl, PHP
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for Prophage Finder

Prophage Finder citations

 (31)
call_split

Complete Genome Sequence of Escherichia coli Strain WG5

2018
Genome Announc
PMCID: 5764933
PMID: 29326209
DOI: 10.1128/genomeA.01403-17
call_split See protocol

[…] 23S), 87 tRNAs, and 22 noncoding RNAs. Multilocus sequence types were identified using MSTL (). No horizontally identified antibiotic resistance genes were detected by using ResFinder (). The PHASTER prophage finder () identified three prophage regions, with two incomplete prophage regions and one questionable prophage region. […]

library_books

Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low temperature survival

2017
BMC Genomics
PMCID: 5460551
PMID: 28583064
DOI: 10.1186/s12864-017-3784-5

[…] B tool (http://softberry.com/), and tRNA genes were detected using the tRNAscan-SE programme []. IS elements were identified using the IS Finder [VC41]. Prophage-associated genes were predicted using Prophage finder (http://phast.wishartlab.com/). The clustered regularly interspaced short palindromic repeats (CRISPRs) were identified using the CRISPRFinder []. Potential virulence factors were dete […]

library_books

Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum

2017
Viruses
PMCID: 5454434
PMID: 28531104
DOI: 10.3390/v9050122

[…] ting 64 different Vibrio species, using CRISPR Finder online tool []. Further, potentially inducible intact prophages were detected in the genomes of our V. anguillarum collection [] using the online prophage finder tool, PHAST []. […]

call_split

Locating and Activating Molecular ‘Time Bombs’: Induction of Mycolata Prophages

2016
PLoS One
PMCID: 4972346
PMID: 27487243
DOI: 10.1371/journal.pone.0159957
call_split See protocol

[…] ccus, and Tsukamurella), and those present are described in detail in and Tables. Putative prophage DNA sequence data were detected using PHAST [], which was preferred over other programs including Prophage Finder [], Prophinder [], and Phage finder [] because of its faster run times, ability to process a wider variety of file types (annotated or un-annotated) of differing completeness (draft or […]

library_books

Genome wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications

2016
BMC Genomics
PMCID: 4756508
PMID: 26884275
DOI: 10.1186/s12864-016-2448-1

[…] Mobile elements were searched in genome sequences. tRNA were identified using tRNA finder. Prophage elements were found using prophage finder (hit per prophage: 4; hit spacing: 3500). Putative insertion sequences were determined using IS finder (minimum score: 80), and manually checked with BLASTP on selected domains in orde […]

library_books

Complete Genome Sequence of Thermus aquaticus Y51MC23

2015
PLoS One
PMCID: 4605624
PMID: 26465632
DOI: 10.1371/journal.pone.0138674

[…] gle contig and annotated using RAST. Likewise, the chromosome of Thermus scotoductus SA-01, ATCC 700910 (NC_014974.1) was re-annotated using RAST. Prophage sequences were identified using the program Prophage Finder [].The evolutionary history of Y51MC23 was inferred by using the maximum likelihood method based on the Tamura-Nei model [] on 16S rDNA sequences. Evolutionary analyses were conducted […]

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Prophage Finder institution(s)
Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI, USA

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