PAIDB

[…] 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 […]

[…] 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., ). […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]