VRprofile

Please use the updated VRprofile2: https://tool2-mml.sjtu.edu.cn/VRprofile

VRprofile

Prediction for virulence factors, antibiotic resistance determinants and transfer-related gene clusters in the genomic sequences of bacterial pathogens. Updated: September-20-2016.
Recommended Browsers: Google Chrome.

Retrieve results

(i) Query bacterial genome

Select genome
Upload sequence
Protein seq (>1)
Upload Contigs

Select a completely sequenced bacterial chromosome from the NCBI genome database

Example: Klebsiella pneumoniae subsp. pneumoniae HS11286 [NC_016845]

or Upload a GenBank file containing one nucleotide sequence and annotation

or Upload a genome sequence file and another CDS annotation file

How to prepare your complete or approximate complete sequence of a given bacterial genome as reference?

or Upload a file containing the multiple protein sequences under analysis.

or (1) Upload a single sequence file containing genome scaffolds or Contigs into 'concatenated-contigs genome'

Optional: (2) Select a Completely Sequenced Reference Bacterial Genome to align and reorder Contigs/Scaffolds to acquire the pseudochromosome using the CDSeasy main program, then submit annotated file into the VRprofile pipeline

(ii) Subject dataset (MobilomeDB)

Gene cluster
Type III secretion systems (T3SS)	Type IV secretion systems (T4SS)
Type VI secretion systems (T6SS)	Type VII secretion systems (T7SS)
Integrative and conjugation elements (ICE)
Prophages
Parameters (Optional) BLASTp E-value HMMer E-value for ICE and prophage detection Minimum number of the significant hits for each prophage-like region Minimum length of the direct repeats of ICE-like region
Single gene
Virulence Factors (VF)	Acquired Antibiotic Resistance Determinants (AR)
Type III secretion effectors (T3SE)	Type IV secretion effectors (T4SE)
Type VI secretion effectors (T6SE)	Type VII secretion effectors (T7SE)
Class I integrons	IS elements (IS)
Parameters (Optional) BLAST [Ha-value]
Genomic island-like region
Pathogenicity islands (PAI)	Antibiotic Resistance Islands (ARI)

(iii) Result retrieval option

Wait for result online; do not close the webpage while running

or Send E-mail notification on job completion to the E-mail address:
please do not close the webpage while data uploading

Microbial Bioinformatics Group at MML, SJTU

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Retrieve results		*VRprofile*
Type in the VRprofile Job_ID