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Genomic island detection software tools | Genome annotation

Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on…
Zisland…
Web
Desktop

Zisland Explorer

Predicts genomic islands based on the segmental cumulative GC profile. Zisland…

Predicts genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic…

MTGIpick
Desktop

MTGIpick

Implements multiscale statistical algorithm to predict genomic islands (GIs)…

Implements multiscale statistical algorithm to predict genomic islands (GIs) from a single genome. MTGIpick uses small-scale test with large-scale features to score small region deviating from the…

IslandViewer
Desktop
Web

IslandViewer

A widely used web-based resource for the prediction and analysis of genomic…

A widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high…

OcculterCut
Desktop

OcculterCut

Measures the local GC-content bias in genomes and a survey of published fungal…

Measures the local GC-content bias in genomes and a survey of published fungal species. OcculterCut identifies species containing distinct AT-rich regions. It can be used to identify genes undergoing…

MSGIP
Desktop

MSGIP Mean Shift Genomic Island Preditor

An automated tool for the prediction of genomic islands (GIs). MSGIP is built…

An automated tool for the prediction of genomic islands (GIs). MSGIP is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the…

xenoGI
Desktop

xenoGI

Identifies and maps genomic islands. xenoGI contains several features: it…

Identifies and maps genomic islands. xenoGI contains several features: it groups genes by origin, identifies islands of genes that entered via common horizontal transfer events, and maps those events…

tRNAcc
Desktop

tRNAcc

A software package to systematically investigate the contents and contexts of…

A software package to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). tRNAcc is ideal for the…

MobilomeFINDER
Web

MobilomeFINDER

An interactive online tool that facilitates bacterial genomic island or…

An interactive online tool that facilitates bacterial genomic island or 'mobile genome' (mobilome) discovery. MobilomeFINDER enables high-throughput island identification and…

Daisy
Desktop

Daisy

Allows mapping-based horizontal gene transfer (HGT) detection. Daisy employs…

Allows mapping-based horizontal gene transfer (HGT) detection. Daisy employs next generation sequencing (NGS) data and is useful in outbreak scenarios of HGT-related pathogens. It does not require a…

SigHunt
Desktop

SigHunt

Identifies genomic regions as candidates for Horizontal gene transfer (HGT)…

Identifies genomic regions as candidates for Horizontal gene transfer (HGT) assessment in eukaryotes. SigHunt is a surrogate method which detects non-ameliorated HGT in large genomic sequences. It is…

Near HGT
Desktop

Near HGT

Identifies putative horizontal gene transfers (HGTs) where the signal is weak.…

Identifies putative horizontal gene transfers (HGTs) where the signal is weak. Near HGT was created on the basis of the notion of synteny index (SI) that is useful in settings of inter-species…

PredictBias
Web

PredictBias

Provides a user-friendly interface that allows researcher to easily analyze the…

Provides a user-friendly interface that allows researcher to easily analyze the location of potential genomic and pathogenicity islands in a prokaryotic genome. PredictBias identifies genomic and…

EDID
Desktop

EDID Ensemble algorithm for Genomic Island Detection

Utilizes the prediction results of existing computational tools, filters and…

Utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between EGID and existing programs have shown that this…

Alien_hunter
Desktop

Alien_hunter

An application for the prediction of putative horizontal gene transfer (HGT)…

An application for the prediction of putative horizontal gene transfer (HGT) events with the implementation of interpolated variable order motifs (IVOMs). An IVOM approach exploits compositional…

IslandPath
Web

IslandPath

A network service which incorporates multiple DNA signals and genome annotation…

A network service which incorporates multiple DNA signals and genome annotation features into a graphical display of a bacterial or archaeal genome, to aid the detection of genomic islands. This is…

GIDetector
Desktop

GIDetector

A software tool that is used to detect genomic islands in prokaryotic genomes.…

A software tool that is used to detect genomic islands in prokaryotic genomes. GIDetector collects prokaryotic genome data from public websites based on users' specification, analyzes genome…

HGTector
Desktop

HGTector

Detects genome-wide vertical versus non-vertical gene history. HGTector is…

Detects genome-wide vertical versus non-vertical gene history. HGTector is based on a statistical analysis of BLAST hit distribution patterns in the context of a priori defined phylogenetic…

COLOMBO/SIGI-HM…
Desktop

COLOMBO/SIGI-HMM

A software framework equipped with a GUI for the statistical analysis of…

A software framework equipped with a GUI for the statistical analysis of sequences of a genome. COLOMBO can be equipped with different plugins that actually perform the analysis. The current version…

IslandPick
Web

IslandPick

A comparative genomics approach that identifies both very probable islands and…

A comparative genomics approach that identifies both very probable islands and non-island regions. The approach involves 1) flexible, automated selection of comparative genomes for each query genome,…

makeCGI
Desktop

makeCGI

An R software package to obtain CpG islands (CGI) from a genome. makeCGI fits…

An R software package to obtain CpG islands (CGI) from a genome. makeCGI fits two HMMs on GC content and obtains posterior probabilities for genomic regions being CpG islands. The CpG islands are…

SPIFinder
Web

SPIFinder

Provides pathogenicity island prediction. SPIFinder is a web application…

Provides pathogenicity island prediction. SPIFinder is a web application identifies Salmonella Pathogenisity Islands in total or partial sequenced isolates of bacteria.

GIST
Desktop

GIST Genomic Island Suite of Tools

A platform for scientific users to predict genomic islands (GIs). GIST includes…

A platform for scientific users to predict genomic islands (GIs). GIST includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an…

GIV
Desktop

GIV Genomic Island Visualization

A visualization tool to displays the locations of genomic islands in a genome,…

A visualization tool to displays the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs, including 1) sequence composition based feature,…

IGIPT
Desktop
Web

IGIPT Integrated Genomic Island Prediction Tool

A web-based integrated platform for the identification of genomic islands…

A web-based integrated platform for the identification of genomic islands (GIs). IGIPT incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus…

GC-Profile
Web

GC-Profile

Provides a method dedicated to analyze the compositional heterogeneity of DNA…

Provides a method dedicated to analyze the compositional heterogeneity of DNA sequences. GC-Profile is an interactive web-based software system with a user-friendly and intuitive input interface. It…

PIPS
Desktop

PIPS Pathogenicity Island Prediction Software

A software suite designed for the prediction of pathogenicity islands. In…

A software suite designed for the prediction of pathogenicity islands. In contrast to other existing tools, PIPS is capable of utilizing multiple features for pathogenicity island detection in an…

PAI-IDA
Desktop

PAI-IDA

A simple method to detect pathogenicity islands and anomalous gene clusters in…

A simple method to detect pathogenicity islands and anomalous gene clusters in bacterial genomes. The method uses iterative discriminant analysis to define genomic regions that deviate most from the…

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