Journal of Integrative Bioinformatics (Jul 2017)

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis

  • Barbosa Eudes,
  • Röttger Richard,
  • Hauschild Anne-Christin,
  • de Castro Soares Siomar,
  • Böcker Sebastian,
  • Azevedo Vasco,
  • Baumbach Jan

DOI
https://doi.org/10.1515/jib-2017-0010
Journal volume & issue
Vol. 14, no. 2
pp. 1366 – 1372

Abstract

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Distinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis). In summary, our strategy aims to identify conserved consecutive homology sequences (islands) in genomes and to identify the most discriminant islands for each lifestyle.

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