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PathogenFinder specifications


Unique identifier OMICS_17865
Name PathogenFinder
Interface Web user interface
Restrictions to use None
Input format FASTA format
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes


  • person_outline Salvatore Cosentino

Publication for PathogenFinder

PathogenFinder citations


Evaluating Different Virulence Traits of Klebsiella pneumoniae Using Dictyostelium discoideum and Zebrafish Larvae as Host Models

PMCID: 5811510
PMID: 29479519
DOI: 10.3389/fcimb.2018.00030

[…] re used as query to search for homologous proteins in each of the analyzed genome, using the NCBI BLAST tools. Identification of virulence factors using whole genome data was performed using the tool PathogenFinder (Cosentino et al., ). […]


Current Bioinformatics resources in combating infectious diseases

PMCID: 5818640
PMID: 29497257
DOI: 10.6026/97320630014031

[…] An important bioinformatics tool to test the pathogenicity of a newly discovered bacterial pathogen is the PathogenFinder 1.1 ( PathogenFinder is a webserver used for the prediction of bacterial pathogenicity utilizing proteomic, genomic, or raw reads. The b […]


Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1

PMCID: 5701452
PMID: 29204271
DOI: 10.1186/s13756-017-0277-x

[…] ov/). In addition, contigs were further annotated using the bacterial bioinformatics database and analysis resource (PATRIC) gene annotation service ( []. The PathogenFinder 1.1 pathogenicity prediction program available at ( was used to examine the nature of P. mirabilis SCDR1 as a human pathogen []. Virulenc […]


Genetic Background and Expression of the New qepA4 Gene Variant Recovered in Clinical TEM 1 and CMY 2 Producing Escherichia coli

Front Microbiol
PMCID: 5640717
PMID: 29062302
DOI: 10.3389/fmicb.2017.01899

[…] bp paired-end reads on a MiSeq (Illumina). Sequence reads were trimmed and filtered according to quality criteria, and de novo assembled into contigs by means of CLC Genomics Workbench 10.0 (QIAGEN). PathogenFinder 1.1, ResFinder 2.1, VirulenceFinder 1.4, SerotypeFinder 1.1, MLST 1.8, pMLST 1.4, and ISSaga were used to estimate the pathogenicity determinants, acquired antibiotic resistance genes, […]


Glimpse into the genome sequence of a multidrug resistant Acinetobacter pittii ST950 clinical isolate carrying the bla OXA 72 and bla OXA 533 genes in China

PMCID: 5607522
PMID: 28954001
DOI: 10.1590/0074-02760170019

[…] nnotation using Subsystem Technology (RAST) server (, ). Classification of predicted proteins in clusters of orthologous groups (COG) functional categories was analysed with the WebMGA web server (). PathogenFinder 1.1, ResFinder 2.1, CARD 2017, VirulenceFinder 1.5, PlasmidFinder 1.3, MLST 1.8 (MultiLocus Sequence Typing), and BacWGSTdb were used to estimate the number of pathogenicity determinant […]


Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry

PMCID: 5554493
PMID: 28848714
DOI: 10.3389/fcimb.2017.00354

[…] ism. The SRST2 pipeline (Inouye et al., ) was used to search for determinants in the ARG-ANNOT antimicrobial resistance database (Gupta et al., ). Putative pathogenicity genes were predicted with the PathogenFinder web-server (Cosentino et al., ) using the “All” model. Blastn was used to search for iron uptake related genes in the C. hepaticus isolate genomes after a DNA database was made with gen […]


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PathogenFinder institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Denmark; National Food Institute, Technical University of Denmark, Denmark
PathogenFinder funding source(s)
This work was supported by the Center for Genomic Epidemiology at the Technical University of Denmark and was funded by grant 09-067103/DSF from the Danish Council for Strategic Research.

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