Comparative Analysis of Genomic Island Prediction Tools

  title={Comparative Analysis of Genomic Island Prediction Tools},
  author={Antonio Camilo da Silva Filho and Roberto Tadeu Raittz and Dieval Guizelini and Camilla Reginatto De Pierri and Di{\^o}nata Willian Augusto and Izabella Castilhos Ribeiro dos Santos-Weiss and Jeroniza N. Marchaukoski},
  journal={Frontiers in Genetics},
Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with other regions in the genome. The goal of this study was to qualitatively and quantitatively evaluate extant genomic island predictors. We chose tools reported to produce… 

Microbial genomic island discovery, visualization and analysis

The main types of GI prediction methods are reviewed and their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing are discussed.

Comparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain.

Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships

This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors.

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

This study proposes to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov.

High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs

Comparisons suggest that H. frisingense has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts, and a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible is suggested.

Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660

The genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp.

Experimental approaches to tracking mobile genetic elements in microbial communities.

How chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities are discussed.

Insights into the Antimicrobial Resistance Profile of a Next Generation Probiotic Akkermansia muciniphila DSM 22959

New insights are provided regarding the phenotypic and genotypic antimicrobial susceptibility profiles of the probiotic candidate A. muciniphila DSM 22959 and no evidence was found of horizontal acquisition or potential transferability of the identified ARG and VF.

The Pan-Genome of the Zoonotic Neglected Pathogen Bartonella henselae Reveals Two Groups with Different Patterns of Adaptation to Hosts

The results point to the need of sequencing more genomes worldwide to better characterize these variations in the pan-genome and understand the patterns of adaptation of this species, which is very important for the development of new vaccines and analyses of drug targets against this pathogen.



Evaluation of genomic island predictors using a comparative genomics approach

The comparative genomics approach, IslandPick, was the most accurate, compared with a curated list of GIs, indicating that it has constructed suitable datasets, and the accuracy of several sequence composition-based GI predictors is evaluated.

Improved genomic island predictions with IslandPath-DIMOB

IslandPath‐DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes.

An Accurate Genomic Island Prediction Method for Sequenced Bacterialand Archaeal Genomes

The development of Genomic Island Hunter (GIHunter), an accurate software tool for GI detection that uses eight GI-associated features such as sequence composition, mobile gene information, and integrase and is shown to be more accurate than other approaches.

Genomic Islands: an overview of current software tools and future improvements

This work states that 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.

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models

SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes that allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.

PredictBias: A Server for the Identification of Genomic and Pathogenicity Islands in Prokaryotes

PredictBias is a web application for the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity with virulence-associated genes and absence in related non-pathogenic species.

GIPSy: Genomic island prediction software.

PIPS: Pathogenicity Island Prediction Software

A novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS) is presented that provides better accuracy than other available software packages and is used to study the veterinary pathogen Corynebacterium pseudotuberculosis.

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

The algorithm identifies tDNAs, finds fragments of those t DNAs in the same replicon and removes unlikely candidate islands through a series of filters, insisting that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

Identification of compositionally distinct regions in genomes using the centroid method

The method, called the centroid approach, can reveal compositionally distinct regions in genomic sequences for any given word size and is demonstrated to identify embedded sequences of varying lengths from distantly related organisms.