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Protocols

PAIDB specifications

Information


Unique identifier OMICS_03204
Name PAIDB
Alternative name PAthogenicity Island DataBase
Restrictions to use None
Version 2.0
Maintained Yes

Publications for PAthogenicity Island DataBase

PAIDB citations

 (13)
library_books

Exploring the Genomic Traits of Non toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

2018
Front Microbiol
PMCID: 5809470
PMID: 29472910
DOI: 10.3389/fmicb.2018.00161

[…] We used PAI finder PAIDB v2.0 (), IslandViewer 4 (), and MAUVE v2.3.1 () to predict the putative genomic islands (GIs) and antimicrobial resistance islands (REIs) in V. parahaemolyticus strains. The criterion of selecti […]

library_books

Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum

2018
PMCID: 5797601
PMID: 29441327
DOI: 10.3389/fcimb.2018.00008

[…] close proximity to known virulence determinants, as well as genes located within Salmonella pathogenicity islands (SPIs) or prophages, were identified and analyzed using Artemis V.14, IslandViewer 3, Pathogenicity Island DataBase (PAIDB v2.0), PHAST and Islander (Rutherford et al., ; Zhou et al., ; Dhillon et al., ; Hudson et al., ; Yoon et al., ). […]

call_split

Locus of Adhesion and Autoaggregation (LAA), a pathogenicity island present in emerging Shiga Toxin–producing Escherichia coli strains

2017
Sci Rep
PMCID: 5539235
PMID: 28765569
DOI: 10.1038/s41598-017-06999-y
call_split See protocol

[…] were determined by analyzing genomic sequences using Unipro GENE and the Geneious software package (v10.0.9; Biomatters Ltd). DNA with PAI features were used to performed BLASTn searches against the Pathogenicity Island Database v2.0. Also, a local BLASTn search was performed in the Geneious software package to determine the distribution of LAA modules and their insertion sites in the genomes ana […]

library_books

IslandViewer 4: expanded prediction of genomic islands for larger scale datasets

2017
Nucleic Acids Res
PMCID: 5570257
PMID: 28472413
DOI: 10.1093/nar/gkx343

[…] grated in IslandViewer (). The IslandViewer webserver also provides precomputed GIs predictions for all microbial genomes available in RefSeq, whereas another resource using similar methodology named PAIDB () focuses on pathogenicity and resistance islands only.The last IslandViewer update, IslandViewer 3, was published in 2015 () and provided a novel interactive and flexible visualization on both […]

library_books

Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach – Identification of pathogen–specific and habitat specific genes

2016
Sci Rep
PMCID: 5141418
PMID: 27924951
DOI: 10.1038/srep38648

[…] To study the distribution of PAI modules in different E. faecalis strains, the 143 kb long PAI sequence of the virulent strain MMH34 was downloaded from PAIDB. Pathogenicity island of E. faecalis is a 143 kb long stretch of bases encoding 129 proteins. The homology conservation of this 143 kb sequence with different strains were analyzed with a suffix […]

call_split

Computational methods for predicting genomic islands in microbial genomes

2016
Comput Struct Biotechnol J
PMCID: 4887561
PMID: 27293536
DOI: 10.1016/j.csbj.2016.05.001
call_split See protocol

[…] er methods. This approach is common for PAI prediction, since it is critical to utilize multiple features to discern PAIs from other GIs. Several PAI detection programs adopt this approach, including PAIDB , PredictBias and PIPS . These programs often combine composition-based methods, comparative genomics methods, and homology-based methods.Both PAIDB and PredictBias firstly identify putative GI […]

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PAIDB institution(s)
Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea Bio-Medical Science Co, Daejeon, Korea; Department of Systems Biology, Yonsei University, Seoul, Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology, Daejeon, Korea

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