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Zisland Explorer specifications

Information


Unique identifier OMICS_11357
Name Zisland Explorer
Interface Web user interface
Restrictions to use None
Input data When performing island prediction, the users only need to submit a standard FASTA sequence file of the genome and optionally upload an annotation file in GenBank ptt style. If the annotation file is unavailable, Zisland Explorer will identify genes using ZCURVE, a gene annotation tool based on Z-curve theory and having been validated on hundreds of genomes.
Output data The users will obtain a file of predicted islands and an image of the cumulative GC profile displaying the predicted islands.
Computer skills Basic
Stability Stable
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_11357
Name Zisland Explorer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data When performing island prediction, the users only need to submit a standard FASTA sequence file of the genome and optionally upload an annotation file in GenBank ptt style. If the annotation file is unavailable, Zisland Explorer will identify genes using ZCURVE, a gene annotation tool based on Z-curve theory and having been validated on hundreds of genomes.
Output data The users will obtain a file of predicted islands and an image of the cumulative GC profile displaying the predicted islands.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Documentation


Maintainer


This tool is not available anymore.

Publication for Zisland Explorer

Zisland Explorer citations

 (4)
library_books

Deciphering pathogenicity and antibiotic resistance islands in methicillin resistant Staphylococcus aureus genomes

2017
Open Biol
PMCID: 5746543
PMID: 29263245
DOI: 10.1098/rsob.170094

[…] of current methods, namely JS-CB (gene clustering based on codon usage bias) [], GIHunter (DGI-database of GIs of 2000 bacterial genomes) [], IslandPick (automated comparative genomics approach) [], Zisland Explorer (based on a segmentation algorithm) [], IslandViewer (database of predicted GIs from three methods) [], PredictBias (based on G + C content, dinucleotide composition, codon usage bias […]

library_books

The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally

2017
Front Microbiol
PMCID: 5449483
PMID: 28620358
DOI: 10.3389/fmicb.2017.00959

[…] ed in genomic islands, or whether they belong to the core-genome we looked for the presence of genomic islands in the chromosome of strain H37Rv, using two bioinformatics tools: IslandViewer 3 () and Zisland Explorer (). The former program identified two islands, while the latter did not identify any. The size of the identified genomic island was of 11,482 base pairs that encode 10 genes (Suppleme […]

call_split

Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering

2016
Front Microbiol
PMCID: 4971588
PMID: 27536294
DOI: 10.3389/fmicb.2016.01210
call_split See protocol

[…] This new tool scans a genome for “leaps” in cumulative GC profile; these atypical regions are annotated GIs ().These parametric methods, with the exception of MJSD and Zisland Explorer, invoke bottom-up approaches, initially classifying genes or sequence windows as alien or native, and then assembling them into GIs or the native genome. […]

call_split

Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post genomic Era

2016
Front Microbiol
PMCID: 4955295
PMID: 27493643
DOI: 10.3389/fmicb.2016.01137
call_split See protocol

[…] iction of protein coding regions and automatic functional annotation was performed using RAST (Rapid Annotations using Subsystem Technology) server version 2.0 (; ). Genomic islands were predicted by Zisland Explorer method (; ). […]


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Zisland Explorer institution(s)
School of Life Sciences, Chongqing University, China; Department of Physics, Tianjin University, China; Bioinformatics Center, University of Electronic Science and Technology of China, China; School of Biomedical Engineering, Tianjin Medical University, China
Zisland Explorer funding source(s)
This work was supported by the National Natural Science Foundation of China (grant numbers 31470068, 31501063, 31171238 and 31571358); Sichuan Youth Science and Technology Foundation of China (2014JQ0051); China National 863 High-Tech Program (2015AA020101); Postdoctoral Science Foundation of China (2015M580211); and Fundamental Research Funds for the Central Universities of China (ZYGX2013J101, ZYGX2015Z006 and ZYGX2015J144).

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