PathogenFinder protocols

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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 in pipelines

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

[…] 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 […]

PMCID: 4424301
PMID: 25953185
DOI: 10.1128/genomeA.00399-15

[…] three genomes for d2-2, chronic_salp, and cp6salp3) consist of 5,982, 5,069, and 5,234 putative genes, respectively, of which 5,590, 4,861, and 5,017 are protein encoding (coding sequences [cdss])., pathogenfinder 1.1 () was used to estimate the number of pathogenic families for each genome. cp6salp3 contains significantly (959) more pathogenic families than d2-2 and chronic_salp (623 and 523, […]

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PathogenFinder in publications

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

[…] 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., )., based in the use of d. discoideum and zebrafish larvae, we set up, optimized, and employed a repertoire of assays to study and compare a set […]

PMCID: 5818640
PMID: 29497257
DOI: 10.6026/97320630014031

[…] available databases for mlst data analysis, mlva typing and slst analysis are given in ., 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. […]

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

[…] 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 []. […]

PMCID: 5645497
PMID: 29081747
DOI: 10.3389/fphar.2017.00724

[…] pipeline (pgap) 4.1 (tatusova et al., ). prophages in the genome were identified using the phage search tool (phast) (zhou et al., ). in addition, pathogenicity of strain cba7126 was predicted using pathogenfinder 1.1 (cosentino et al., ). carbohydrate-active enzymes were annotated using dbcan (yin et al., )., to identify the unique features of strain cba7126, the genomes of b. licheniformis […]

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

[…] 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, […]

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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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