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Genomic Islands: an overview of current software and future improvements

de Castro Soares, Siomar ; de Castro Oliveira, Leti­cia ; Kumar Jaiswal, Arun ; Azevedo, Vasco

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth´s biomass and new predictions point for the existence of 10^11 to 10^12 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
de Castro Soares, Siomar ; de Castro Oliveira, Leti­cia ; Kumar Jaiswal, Arun ; Azevedo, Vasco  (2016)  Genomic Islands: an overview of current software and future improvements. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 13(1), 2016

Online-Journal: http://journal.imbio.de/article.php?aid=301
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2017/5437



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