Welcome1 to PHISDetector

Phage-host interactions are appealing systems to study bacterial adaptive evolution and are increasingly recognized as playing an important role in human health and diseases, which may contribute to novel therapeutic agents, such as phage therapy to combat multi-drug resistant infections.

PHISDetector, a web tool to detect and systematically study diverse in silico phage-host interaction signals, including analyses for Sequence composition, CRISPR, Prophage, Genetic homology and protein-protein interactions. PHISDetector uses two criteria to predict phage-host interactions and integrates all Phage-Host Interaction Signals(PHIS) analysis into a PHIE module with machine learning models. PHISDetector accepts various genomics as input and provides well-designed and interactive visualization graphics and detailed data tables to download for each PHIS signal.

PHISDetector also provides analysis for oligonucleotide profile/sequence composition,CRISPR-targeting, Prophages, phage genome similarity, special gene check, protein-protein interactions and co-occurrence/co-abundance patterns in Tools.

Detect diverse in silico phage-host interaction signals

Assess for problematic genes

Protein Interaction


Recent works from our group:

1. Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Nature. DOI:10.1038/nature22377.

2. Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA. Cell Research. doi:10.1038/cr.2017.46.

3. Crystal structure of CRISPR-Cpf1 in complex with CRISPR RNA (crRNA). Nature. 532, 522-526.

4. Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins.[J].Bmc Biology, 2018, 16(1):32.

5. CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. Communications Biology 1, 180, doi:10.1038/s42003-018-0184-6 (2018).

Resource Links

CRISPRMiner

http://www.microbiome-bigdata.com/CRISPRminer

CRISPRCasFinder

https://crisprcas.i2bc.paris-saclay.fr/Home/

PILER

http://www.drive5.com/pilercr/

WiSH

https://github.com/soedinglab/wish

VirHostMatcher

https://github.com/jessieren/VirHostMatcher

HostPhinder

https://github.com/julvi/HostPhinder

GeneNet

https://github.com/coevoeco/GeneNet

PHASTER

http://phaster.ca/

VirSorter

https://github.com/simroux/VirSorter

Phage_Finder

http://phage-finder.sourceforge.net/

ShortBRED

https://bitbucket.org/biobakery/shortbred/src

RGI

https://github.com/arpcard/rgi

DIAMOND

https://github.com/bbuchfink/diamond

BLAST

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/

FragGeneScan

https://sourceforge.net/projects/fraggenescan/