SPIFinder protocols

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SPIFinder specifications

Information


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 in pipeline

2017
PMCID: 5646404
PMID: 29051251
DOI: 10.1128/genomeA.01119-17

[…] 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 […]


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SPIFinder in publications

 (4)
PMCID: 5934421
PMID: 29755416
DOI: 10.3389/fmicb.2018.00616

[…] 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., the complete genome of s. typhimurium ww012 […]

PMCID: 5690322
PMID: 29146845
DOI: 10.1128/genomeA.01128-17

[…] 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 […]

PMCID: 5624768
PMID: 28963222
DOI: 10.1128/genomeA.01061-17

[…] 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 […]

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

[…] 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 (). […]


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