Detecting genomic islands using bioinformatics approaches

MGI Langille, WWL Hsiao, FSL Brinkman - Nature Reviews …, 2010 - nature.com
Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called
genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of …

Microbial genomic island discovery, visualization and analysis

C Bertelli, KE Tilley, FSL Brinkman - Briefings in bioinformatics, 2019 - academic.oup.com
Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for
microbial genome evolution, enabling rapid adaptation and survival in specific niches …

Improved genomic island predictions with IslandPath-DIMOB

C Bertelli, FSL Brinkman - Bioinformatics, 2018 - academic.oup.com
Abstract Motivation Genomic islands (GIs) are clusters of genes of probable horizontal origin
that play a major role in bacterial and archaeal genome evolution and microbial adaptability …

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

J Li, C Tai, Z Deng, W Zhong, Y He… - Briefings in …, 2018 - academic.oup.com
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic
resistance genes, as well as extends these trait transfer-related genetic contexts, in newly …

Genomic Island Prediction via Chi‐Square Test and Random Forest Algorithm

M Onesime, Z Yang, Q Dai - Computational and Mathematical …, 2021 - Wiley Online Library
Genomic islands are related to microbial adaptation and carry different genomic
characteristics from the host. Therefore, many methods have been proposed to detect …

Leveraging comparative genomics to uncover alien genes in bacterial genomes

S Sengupta, RK Azad - Microbial Genomics, 2023 - microbiologyresearch.org
A significant challenge in bacterial genomics is to catalogue genes acquired through the
evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and …

2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome

R Kong, X Xu, X Liu, P He, MQ Zhang, Q Dai - BMC bioinformatics, 2020 - Springer
Background Genomic islands are associated with microbial adaptations, carrying genomic
signatures different from the host. Some methods perform an overall test to identify genomic …

Identify Golgi protein types with modified mahalanobis discriminant algorithm and pseudo amino acid composition

H Ding, L Liu, FB Guo, J Huang… - Protein and peptide …, 2011 - ingentaconnect.com
The Golgi apparatus is an important eukaryotic organelle. Successful prediction of Golgi
protein types can provide valuable information for elucidating protein functions involved in …

Comparative analysis of genomic island prediction tools

AC da Silva Filho, RT Raittz, D Guizelini… - Frontiers in …, 2018 - frontiersin.org
Tools for genomic island prediction use strategies for genomic comparison analysis and
sequence composition analysis. The goal of comparative analysis is to identify unique …

MTGIpick allows robust identification of genomic islands from a single genome

Q Dai, C Bao, Y Hai, S Ma, T Zhou… - Briefings in …, 2018 - academic.oup.com
Genomic islands (GIs) that are associated with microbial adaptations and carry sequence
patterns different from that of the host are sporadically distributed among closely related …