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Protocols

Prophinder specifications

Information


Unique identifier OMICS_11704
Name Prophinder
Interface Web user interface, Application programming interface
Restrictions to use None
Input data The algorithm takes as input, a prokaryotic genome sequence in GenBank format with annotated positions of genes and coding sequences (CDSs).
Input format GenBank
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Gipsi Lima-Mendez

Publication for Prophinder

Prophinder citations

 (42)
library_books

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

2017
BMC Genomics
PMCID: 5644110
PMID: 29037147
DOI: 10.1186/s12864-017-4165-9

[…] tandard settings with GFF3 annotation files generated by PROKKA [] used as input files. The genomic islands were detected with the help of IslandViewer 3 software []. For the prediction of prophages, Prophinder [] and Phaster [] online software were used. Predicted bacteriophages were then reviewed visually for structural completeness.Prediction of CRISPR loci was aided by the CRISPRFinder []. The […]

library_books

A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437

2017
Sci Rep
PMCID: 5567305
PMID: 28831124
DOI: 10.1038/s41598-017-09317-8

[…] The genomes of the selected Paraburkholderia strains were screened for the presence of prophages by using PHAST- version October 2015, Prophinder/ACLAME- version 04, October 2015 and PhiSpy [PhiSpyNov11_3.2]. PHAST and Prophinder identify prophage regions by using a database of known phage genes, sequence identification, tRNA identif […]

library_books

Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

2017
BMC Genomics
PMCID: 5467263
PMID: 28606056
DOI: 10.1186/s12864-017-3842-z

[…] Prophages in the genome of P. aeruginosa ATCC 27853 were predicted using the online softwares Prophinder with parameters (Scanning window size: 20,50,100,200,300; Minimum nb of CDS in prophages: 20; Minimum nb of ACLAME hits: 20; Blast Eval threshold: 1e-5; Minimum DR size: 10) [] and PHAST [] […]

library_books

Intriguing Interaction of Bacteriophage Host Association: An Understanding in the Era of Omics

2017
Front Microbiol
PMCID: 5383658
PMID: 28439260
DOI: 10.3389/fmicb.2017.00559

[…] es with reference bacteria genome may reveal a prophage viral element using “recruitment plot” in the bacterial genome. Some of the bioinformatics tools adapted for prophage detection include ACLAME, Prophinder, PHAST and PhiSpy which can serve in confirming phage annotation (Akhter et al., ).Along with elucidating diversity and taxonomy of phages, establishing the origin of genes (bacterial or vi […]

library_books

Insights of Phage Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

2017
Front Microbiol
PMCID: 5334351
PMID: 28316597
DOI: 10.3389/fmicb.2017.00352

[…] etic elements including prophages, plasmids, and transposons were investigated in the prokaryote contigs. Following gene prediction in the prokaryote contigs, integrated prophages were detected using Prophinder (Lima-Mendez et al., ) to identify mobile genetic elements. Simultaneously, in order to relate the prophages to their host, prokaryote contigs were compared against ACLAME (A CLAssification […]

library_books

Genome wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

2016
BMC Evol Biol
PMCID: 5122149
PMID: 27881071
DOI: 10.1186/s12862-016-0815-9

[…] core surrounding regions shared by all proximate species (syntenic shared blocks). Predictions concerning genomic islands were retrieved from IslandViewer [] and predicted prophages were sourced from Prophinder []. A G + C content analysis was performed with overlapping sliding windows of 1000 bp at a step of 30 bp using JaDis []. […]


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Prophinder institution(s)
Laboratoire de Bioinformatique des Génomes et des Réseaux, Université Libre de Bruxelles, Bruxelles, Belgium
Prophinder funding source(s)
This work is supported by ESA-PRODEX (contract C90254), the Fonds de la Recherche Fondamentale Collective, the Actions de Recherche Concertés du Ministre de la Communauté Française de Belgique and the Université Libre de Bruxelles.

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