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Protocols

GIHunter specifications

Information


Unique identifier OMICS_29853
Name GIHunter
Alternative name Genomic Island Hunter
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Dongsheng Che

Publication for Genomic Island Hunter

GIHunter citations

 (3)
call_split

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

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

[…] Genomic Island Hunter (GIHunter) [] uses a decision tree to identify GIs. It builds a GI/non-GI gene classifier using the dataset of known GIs and non-GIs. GI features, such as sequence composition, p […]

call_split

Computational methods for predicting genomic islands in microbial genomes

2016
Comput Struct Biotechnol J
PMCID: 4887561
PMID: 27293536
DOI: 10.1016/j.csbj.2016.05.001
call_split See protocol

[…] orporating more precise annotations available now .Several machine learning approaches based on constructed GI datasets have been proposed, including Relevance Vector Machine (RVM) , GIDetector , and GIHunter . The major differences among them are in the choices of training datasets, GI-related features, and learning algorithms.RVM is the first machine learning method to study structural models of […]

library_books

A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes

2014
PMCID: 4897231
PMID: 27433520
DOI: 10.1155/2014/732857

[…] leotide biases, codon usage, mobility genes (including transposases and integrases), and tRNA genes [, ]. Related tools using this kind of approach include AlienHunter [], Centroid [], GIDetector [], GIHunter [], PAI IDA [], and SIGI-HMM []. Comparative genome approach uses the phylogenetically close species as reference genomes and identifies subsequences that are unique in the query genomes and […]

Citations

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GIHunter institution(s)
Department of Computer Science, East Stroudsburg University, East Stroudsburg, PA, USA; Computer Science Department, University of Central Arkansas, Conway, AR, USA
GIHunter funding source(s)
Supported by President Research Fund, Faculty Professional Development & Research (FDR) major grant, and FDR mini grant at East Stroudsburg University, USA.

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