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ISfinder specifications

Information


Unique identifier OMICS_03195
Name ISfinder
Alternative names Insertion Sequences finder, ISbrowser
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Allowed
Version 1.0
Maintained Yes

Maintainer


  • person_outline Mick Chandler

Additional information


https://www-is.biotoul.fr/about.php

Publications for Insertion Sequences finder

ISfinder citations

 (155)
call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] eins (NR) database, Pfam, and Interpro scan were used to assess their putative functions by identification of structural features and motifs,. ResFinder (version 2.1), PlasmidFinder (version 1.3) and ISfinder were used to determine the presence of resistance genes, replicon types and insertion sequences, respectively–. Plasmid sequences were hierarchically clustered and displayed as a phenogram us […]

library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] genome were identified and categorized (intact, incomplete or questionable) using the PHASTER website (http://phaster.ca/) []. Insertion sequences located within the genome were identified using the ISfinder website (https://www-is.biotoul.fr/) [] using a cutoff of 75% identity across 75% of the insertion sequence. Additionally, each of the genomes was manually reviewed for the presence of transp […]

library_books

Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe

2018
Front Microbiol
PMCID: 5895724
PMID: 29675009
DOI: 10.3389/fmicb.2018.00656

[…] imer walking approach. Once completed, the genomes were aligned with Mauve (Darling et al., ) and MUMmer (Delcher et al., ). The insertion thus identified were exported and annotated using Blast, the ISFinder database (Siguier et al., ), and the annotation service of Insertion Sequences (IS) provided by the ISsaga (Insertion Sequence semi-automatic genome annotation) engine (Varani et al., ).Reads […]

library_books

Genomic Analysis of a Pan Resistant Isolate of Klebsiella pneumoniae, USA 2016

2018
MBio
PMCID: 5885025
PMID: 29615503
DOI: 10.1128/mBio.00440-18

[…] 21 (). Acquired antimicrobial resistance genes were identified on high-quality contigs using the Resfinder repository () and SSTAR V1.1.01 (). Finally, additional genes were detected with PGAP () and ISfinder () to identify genes contributing to displayed phenotypic resistance which could not be explained by acquired mechanisms present in the Resfinder collection alone.The sequenced K. pneumoniae […]

call_split

Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase 48–Like Carbapenemases, USA

2018
PMCID: 5875285
PMID: 29553324
DOI: 10.3201/eid2404.171377
call_split See protocol

[…] osciences contigs to estimate the plasmid composition of each isolate (). In addition, we predicted insertion sequences that might be associated with spread of antimicrobial resistance genes by using ISfinder (). For isolates with blaOXA-48, we estimated the copy number of IS1R insertion sequences for determining Tn1999 variants by using blastn (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and SPAdes […]

library_books

Genome Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships

2018
PMCID: 5940136
PMID: 29602809
DOI: 10.1534/g3.118.200018

[…] ryotic Genome Annotation Pipeline on the GenBank database. Genomic islands, insertion sequences, interspersed repetitive sequences, and tandem repeats were predicted with IslandPath-DIOMB program (), ISfinder (https://www-is.biotoul.fr/), RepeatMasker v4.0.5 (), and TRF v4.0.7b () with default parameters, respectively.Functional annotations were conducted by BLASTP algorithm similarity search agai […]

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ISfinder institution(s)
Laboratoire de Microbiologie et Génétique Moléculaires, C.N.R.S., Toulouse, France

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