Related Experiment Video
Updated: May 11, 2026
10:30
High-throughput Analysis of Locomotor Behavior in the Drosophila Island Assay
Published on: November 5, 2017
IslandViewer update: Improved genomic island discovery and visualization.
Bhavjinder K Dhillon1, Terry A Chiu, Matthew R Laird
1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
Nucleic Acids Research
|May 17, 2013
Summary
IslandViewer is an enhanced web tool for predicting genomic islands (GIs) in microbes. It now offers improved efficiency, custom analysis options, and comparative visualization for GIs.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Genomic islands (GIs) are crucial for microbial adaptation, often carrying genes for virulence and antibiotic resistance.
- Accurate prediction of GIs is essential for understanding microbial evolution and pathogenicity.
- Existing tools for GI prediction vary in accuracy and integration.
Purpose of the Study:
- To report recent improvements to the IslandViewer web application for predicting genomic islands.
- To enhance the efficiency and user-friendliness of GI analysis in bacterial and archaeal genomes.
- To provide advanced features for custom analysis, annotation overlay, and genome comparison.
Main Methods:
- Integration of three leading GI prediction algorithms: IslandPath-DIMOB, SIGI-HMM, and IslandPick.
- Precomputation of GI predictions for all complete microbial genomes available at NCBI.
- Development of an enhanced framework for user-uploaded genomes and customized analysis settings.
- Implementation of features for overlaying virulence factors, antibiotic resistance genes, and pathogen-associated genes.
- Introduction of a side-by-side viewer for comparing GIs between selected genomes.
Main Results:
- Significant improvements in the efficiency of the IslandViewer framework to handle increased user load.
- Enhanced capabilities for custom genome analyses with flexible settings.
- Expanded annotation options, including virulence factors and antibiotic resistance genes, overlaid on GI predictions.
- Facilitation of comparative genomic island analysis through a new side-by-side viewer.
Conclusions:
- The updated IslandViewer provides a more efficient and flexible platform for genomic island analysis.
- Additional annotation layers and comparative tools enhance the utility of IslandViewer for diverse microbial studies.
- These improvements aid researchers in analyzing the medical, environmental, and industrial relevance of genomic islands.
Related Concept Videos
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:31In-situ Hybridization
In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.