Prophinder protocols

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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 in pipelines

 (2)
2016
PMCID: 4725956
PMID: 26808278
DOI: 10.1371/journal.pone.0146832

[…] manually in more detail., furthermore, a blastp search against the aclame database ([], http://aclame.ulb.ac.be/; 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 […]

2010
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 []http://aclame.ulb.ac.be/tools/prophinder/, and cgview were used to determine the origin of the circular genome, identify prophages, and to obtain a circular graphical representation […]


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Prophinder in publications

 (37)
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. […]


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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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