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SPIFinder specifications


Unique identifier OMICS_21967
Name SPIFinder
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data An uncompressed database of DNA sequences.
Input format FASTA
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

SPIFinder citations


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

Front Microbiol
PMCID: 5934421
PMID: 29755416
DOI: 10.3389/fmicb.2018.00616
call_split See protocol

[…] 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

Genome Announc
PMCID: 5690322
PMID: 29146845
DOI: 10.1128/genomeA.01128-17
call_split See protocol

[…] 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┬áMb, 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

Genome Announc
PMCID: 5646404
PMID: 29051251
DOI: 10.1128/genomeA.01119-17
call_split See protocol

[…] 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

Genome Announc
PMCID: 5624768
PMID: 28963222
DOI: 10.1128/genomeA.01061-17
call_split See protocol

[…] 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

PLoS Curr
PMCID: 5145817
PMID: 28018748
DOI: 10.1371/currents.outbreaks.1bb3e36e74bd5779bc43ac3a8dae52e6

[…] 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?

PMCID: 5069764
PMID: 27822532
DOI: 10.1128/mSystems.00009-16

[…] 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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