IslandHunter – A Java-based GI detection software
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Abstract
Over the past decade, researchers have discovered that apart from the essential genes, bacterial genomes also contain a variable amount of accessory genes acquired by horizontal gene transfer (HGT) that are categorized as genomic islands (GIs). GIs encode adaptive traits, which might be beneficial for the species under certain growth or environmental conditions. It has always been a challenge for biologists to identify GIs within a bacterial genome as they evolve very rapidly. This paper proposes a standalone software, IslanHunter, that has been developed using Java and BioJava and can extract GI regions using GC content, codon usage bias, dinucleotide frequency bias, tetranucleotide frequency bias, k-mer signature analysis (2-mer, 3-mer, 4-mer, 5-mer, and 6-mer) and presence of mobility genes. IslandHunter provides a simple graphical user interface where disclosed GIs are displayed in a tree-view and a circular graph. Users are presented with options to save the GI regions as blocks of DNA sequences in FASTA format. They can later use these predicted GI regions for further analysis. IslandHunter can take as input, files in GenBank, EMBL or FASTA formats. IslandHunter provides flexible display options and save options. The software has been evaluated against exiting tools with good performance. It is available for evaluation at https://github.com/ShakunBaichoo/IslandHunter .
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2014. IslandHunter – A Java-based GI detection software. PeerJ PrePrints 2:e716v1 https://doi.org/10.7287/peerj.preprints.716v1Author comment
This is a submission to PeerJ for review.
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Competing Interests
The authors declare they have no competing interests.
Author Contributions
Shakuntala Baichoo conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.
Haswanee Goodur conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Vyasanand Ramtohul conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Funding
The authors declare there was no funding for this work.
