Tool stats & trends
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|Interface||Web user interface|
|Restrictions to use||None|
|Input data||An uncompressed database of DNA sequences.|
Complete Genomic Analysis of a Salmonella enterica Serovar Typhimurium Isolate Cultured From Ready to Eat Pork in China Carrying One Large Plasmid Containing mcr 1
[…] 3382.1), and Salmonella Indiana C629 (Accession number CP015724) were available from GenBank and used to compare the Salmonella pathogenicity islands (SPIs) with S. Typhimurium WW012 in this study by SPIFinder. Finally, the antibacterial biocide and metal resistance genes database (BacMet) was used to predict the presence of any metal-resistance genes. […]
Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in Ibadan, Nigeria, Representing 21 Salmonella Serovars
[…] s. In silico multilocus sequence typing (MLST) data were extracted from the Enterobase online tool (http://enterobase.warwick.ac.uk). Salmonella pathogenicity islands (SPIs) were identified using the SPIFinder version 1.0 online tool (https://cge.cbs.dtu.dk/services/SPIFinder). The total lengths of these genomes range from 4.6 to 5.2 Mb, with an average GC content of 52%, and the numbers of contig […]
Genome Sequences of Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the USA
[…] mum alignment length set at 100% (). Homologues of Salmonella pathogenicity islands (SPI) 1, 2, 3, 4, and 8 as well as the centisome 63 pathogenicity island (C63PI) were detected in all genomes using SPIFinder with default parameters (http://www.genomicepidemiology.org/). Clustered regularly interspaced short palindromic repeat (CRISPR) types identified in Enterobase were 1,097 (isolates CFSAN0117 […]
Draft Genome Sequences of Biofilm Forming and Non Biofilm Forming Nontyphoidal Salmonella enterica Serovars
[…] mids on assembled sequences were predicted using ResFinder version 2.1 (), CRISPRFinder (http://crispr.i2bc.paris-saclay.fr/Server/), PHAST (), SPI Finder version 1.0 (https://cge.cbs.dtu.dk/services/SPIFinder), and PlasmidFinder version 1.3 (), respectively ().Our data reveal that biofilm-forming NTS strains have larger genome sizes and increased coding sequences (CDSs) relative to non-biofilm fo […]
Laboratory Investigation of Salmonella enterica serovar Poona Outbreak in California: Comparison of Pulsed Field Gel Electrophoresis (PFGE) and Whole Genome Sequencing (WGS) Results
[…] using the CGE online tool against the 7-gene MLST database of University of Warwick (http://mlst.warwick.ac.uk/mlst/dbs/Senterica). The Salmonella Pathogenicity Islands (SPI) were characterized using SPIFinder 1.0 CGE tool (https://cge.cbs.dtu.dk/services/SPIFinder/).Paired-end reads were mapped to the de novo assembled outbreak Salmonella Poona M15X04725 draft genome (48 contigs, N50= 223,917) us […]
Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction Modification Systems?
[…] lly available online tools were developed. Both tools, Restriction-ModificationFinder (https://cge.cbs.dtu.dk/services/Restriction-ModificationFinder/) and SPI-Finder (https://cge.cbs.dtu.dk/services/SPIFinder/), were built on a BLAST-based methodology for detection of genes from customized databases, originally developed by Zankari et al. for in silico detection of acquired resistance genes (). T […]
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