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Prophage Finder specifications

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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

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Publication for Prophage Finder

Prophage Finder citations

 (23)
library_books

Complete Genome Sequence of Escherichia coli Strain WG5

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

[…] 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., the genome sequences have been deposited in genbank […]

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

[…] 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 […]

library_books

Complete Genome Sequence of Thermus aquaticus Y51MC23

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

[…] 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 […]

library_books

Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle

2015
PLoS One
PMCID: 4551802
PMID: 26313942
DOI: 10.1371/journal.pone.0136101

[…] categories to the repertoire of predicted proteins of the b728a, dc3000 and 1448a strains. predictions of horizontally transferred regions and prophages were computed using alien hunter 1.7 [] and prophage finder [], respectively. t346hunter [] was used to identify secretion systems clusters., the distribution of all 64 trinucleotides was determined for the whole chromosome and 2 kb […]

library_books

Genome scale resources for Thermoanaerobacterium saccharolyticum

2015
BMC Syst Biol
PMCID: 4518999
PMID: 26111937
DOI: 10.1186/s12918-015-0159-x

[…] further supporting its identification as an extra-chromosomal unit []., the genome contains 39 orfs predicted to have transposase function, with 12 of these concentrated in a 50 kbp region. the tool prophage finder [] was used to identify two regions containing genes with similarity to known phage genes using the software’s strict search settings (e-value cut off = 0.001). these two regions […]

library_books

Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees

2015
Genome Biol Evol
PMCID: 4494060
PMID: 25953738
DOI: 10.1093/gbe/evv079

[…] than chromosomes when searches was performed using blastn or tblastx against the nt database, and 4) presence of genes with putative plasmid origin. prophages were detected with phast () and prophage finder (). prophage finder was first tested with default parameters and second with a more strict e value threshold (1e-3). phast served as confirmation for some of the regions detected […]


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

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