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Protocols

INTEGRALL specifications

Information


Unique identifier OMICS_03921
Name INTEGRALL
Restrictions to use None
Database management system MySQL
Version 1.2
Maintained Yes

Maintainer


  • person_outline INTEGRALL

Publication for INTEGRALL

INTEGRALL citations

 (20)
library_books

Human Activity Determines the Presence of Integron Associated and Antibiotic Resistance Genes in Southwestern British Columbia

2018
Front Microbiol
PMCID: 5938356
PMID: 29765365
DOI: 10.3389/fmicb.2018.00852

[…] ssembled and unassembled pairs using MEGAHIT () and contigs shorter than 200 nt were discarded. Nucleotide sequences were aligned against the comprehensive antibiotic resistance database (CARD; ) and Integrall () using BLAST (). […]

library_books

Discovery of the fourth mobile sulfonamide resistance gene

2017
Microbiome
PMCID: 5732528
PMID: 29246178
DOI: 10.1186/s40168-017-0379-y

[…] fferent classes of antibiotics is indicated in Table . Moreover, to assess if the identified ORFs included genes that were not previously described as integron gene cassettes, we matched them against INTEGRALL []. Of the 19,723 non-redundant ORFs identified in this study, 5942 (~ 30%) were previously reported (see the section). However, the rest of the ORFs had lower nucleotide similarity (identi […]

library_books

Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland

2017
Front Microbiol
PMCID: 5641379
PMID: 29067005
DOI: 10.3389/fmicb.2017.01922

[…] lity groups were identified using PlasmidFinder 1.3 and specific plasmid multi-locus sequence type (pMLST) was identified with pMLST-1.4 (). Insertion sequences were identified using ISFinder (), and INTEGRALL was used to identify integrons and gene cassettes ().Phylogenetic analysis of the amino acid sequence of the AmpC-like β-lactamase found on plasmid pLNU-11 was performed using MEGA v. 7 () u […]

call_split

Co occurrence of 3 different resistance plasmids in a multi drug resistant Cronobacter sakazakii isolate causing neonatal infections

2017
PMCID: 5955447
PMID: 28771073
DOI: 10.1080/21505594.2017.1356537
call_split See protocol

[…] with BLASTP/BLASTN searches against the UniProtKB/Swiss-Prot and RefSeq databases. Annotation of resistance genes, mobile elements and other features was performed using CARD, ResFinder, ISfinder and INTEGRALL. Multiple and pairwise sequence comparisons were performed using MUSCLE 3.8.31 and BLASTN, respectively. Gene organization diagrams were drawn in Inkscape 0.48.1. […]

call_split

pSY153 MDR, a p12969 DIM related mega plasmid carrying blaIMP 45 and armA, from clinical Pseudomonas putida

2017
Oncotarget
PMCID: 5620268
PMID: 28978128
DOI: 10.18632/oncotarget.19496
call_split See protocol

[…] [] searches against the UniProtKB/Swiss-Prot [] and RefSeq [] databases. Annotation of resistance genes, mobile elements, and other features was carried out using CARD [], ResFinder [], ISfinder [], INTEGRALL []. Multiple and pairwise sequence comparisons were performed using MUSCLE 3.8.31 [] and BLASTN, respectively. Gene organization diagrams were drawn in Inkscape (https://inkscape.org). […]

call_split

Genomic characterization of novel IncFII type multidrug resistant plasmids p0716 KPC and p12181 KPC from Klebsiella pneumoniae

2017
Sci Rep
PMCID: 5517477
PMID: 28725038
DOI: 10.1038/s41598-017-06283-z
call_split See protocol

[…] with BLASTP/BLASTN searches against the UniProtKB/Swiss-Prot and RefSeq databases. Annotation of resistance genes, mobile elements, and other features was carried out using CARD, ResFinder, ISfinder, INTEGRALL, and the Tn Number Registry. Multiple and pairwise sequence comparisons were performed using MUSCLE 3.8.31 and BLASTN, respectively. Gene organization diagrams were drawn in Inkscape 0.48.1. […]

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INTEGRALL institution(s)
CESAM & Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro; Sindesi – Informatic Systems and Solutions Lda., Aveiro; Department of Biology, University of Aveiro, Campus Universitário de Santiago, Portugal

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