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J Integr Bioinform. 2017 Jul 5;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0010/jib-2017-0010.xml. doi: 10.1515/jib-2017-0010.

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

Abstract

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.

KEYWORDS:

Bacteria; Homologous genes; Island; Lifestyle; Machine Learning

PMID:
28678736
PMCID:
PMC6042826
DOI:
10.1515/jib-2017-0010
[Indexed for MEDLINE]
Free PMC Article

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