Prophinder protocols

View Prophinder computational protocol

Prophinder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Prophage prediction chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

Prophinder specifications


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


  • person_outline Gipsi Lima-Mendez <>

Publication for Prophinder

Prophinder in pipelines

PMCID: 4725956
PMID: 26808278
DOI: 10.1371/journal.pone.0146832

[…] manually in more detail., furthermore, a blastp search against the aclame database ([],; accessed 31 march 2015) was conducted to detect virus and prophage-associated genes (prophinder, []) using default settings., the nearly complete genome sequence of “ferrovum” strain ja12 is accessible at ddbj/embl/genbank under the accession number ljwx00000000., mrs beate erler […]

PMCID: 3091675
PMID: 20863402
DOI: 10.1186/1471-2164-11-511

[…] to ncbi, comprehensive microbial resource (cmr) and integrated microbial genomes (img) were used to compare om5 against all of the publicly available, complete prokaryotic genomes. orifinder, prophinder [], and cgview were used to determine the origin of the circular genome, identify prophages, and to obtain a circular graphical representation […]

To access a full list of citations, you will need to upgrade to our premium service.

Prophinder in publications

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

[…] and a quaternary ammonium compound-resistance protein suge (pfr_js23_1469).fig. 6 , all the genomes were checked for additional prophage sequences with two dedicated programs: phaster and prophinder. from the candidate prophages, only the prophage from the strain js17 appeared complete. the prophage js17 is located between the trna-ser(tga) gene and a transposase gene […]

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

[…] as well as of p. phytofirmans strains bs455, bifas53, j1u5 and psjn, for the presence of putative prophage-like (pp) elements (table ). for this, we used the phage identification programs phast, prophinder/aclame and phispy. by applying the criteria (see material and methods), we identified a total of 209 pp regions across the eight paraburkholderia genomes. following curation, 127 […]

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

[…] were not annotated as they only displayed high similarity to certain genes present in a handful of draft genomes of p. aeruginosa strains that lack functional annotation., prophage prediction using prophinder [] and phast [] revealed seven prophages in the genome of p. aeruginosa atcc 27853. all these prophages were assigned as accessory genes and are designated as prophage 1–7 (table , fig. ). […]

PMCID: 5334351
PMID: 28316597
DOI: 10.3389/fmicb.2017.00352

[…] 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 […]

PMCID: 5122149
PMID: 27881071
DOI: 10.1186/s12862-016-0815-9

[…] 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 []., additional file 1: table s1. additional file 2: table s2. […]

To access a full list of publications, you will need to upgrade to our premium service.

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.

Prophinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Prophinder