Prophage Finder protocols

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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

Maintainer


This tool is not available anymore.

Publication for Prophage Finder

Prophage Finder in pipelines

 (3)
2015
PMCID: 4374763
PMID: 25811873
DOI: 10.1371/journal.pone.0120759

[…] the best hit for every phage protein was determined (). hits with similarity < 30% were discarded., the genome sequence of b. licheniformis dsm13 was initially scanned with the prediction tool prophage finder []. the nine predicted prophage regions were evaluated based on a set of genomic features and thus, seven regions were annotated as prophage regions bli_pp1 – bli_pp7 (access code […]

2015
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 […]

2013
PMCID: 3787669
PMID: 23918808
DOI: 10.1093/gbe/evt117

[…] and manual correction performed by in silico molecular cloning (in silico biology, inc.). prophage regions and clustered regularly interspaced short palindromic repeats (cripsrs) were identified by prophage finder () and crisprfinder (), respectively., whole-genome sequences were aligned with mafft (). the evolutionary model (simple hyk) was chosen based on the results obtained with jmodeltest […]

Prophage Finder in publications

 (23)
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 […]

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 […]

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 […]

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 […]

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 […]

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

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