Related Experiment Video
Updated: Jul 19, 2026
22:27
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
Genomes as geography: using GIS technology to build interactive genome feature maps.
Mary E Dolan1, Constance C Holden, M Kate Beard
1National Center for Geographic Information and Analysis, University of Maine, Orono, ME 04469, USA. mdolan@informatics.jax.org
BMC Bioinformatics
|September 21, 2006
Summary
Genome Spatial Information System (GenoSIS) applies geographic information system (GIS) technology for advanced genome data visualization and querying. This novel approach enables dynamic genome map generation and complex spatial analysis beyond traditional genome browsers.
Area of Science:
- Bioinformatics
- Genomics
- Geographic Information Systems (GIS)
Background:
- Traditional genome browsers use horizontal data tracks and limited keyword searches.
- Existing browsers restrict detailed annotation display to single genomic regions.
- There is a need for more advanced genome data interaction and visualization methods.
Purpose of the Study:
- To develop a Genome Spatial Information System (GenoSIS) for spatial genome data display and interaction.
- To leverage Geographic Information System (GIS) concepts for genome data management.
- To enable complex attribute and spatial queries for genome features.
Main Methods:
- Adapted GIS methodologies and tools for genome data representation.
- Developed GenoSIS using ArcGIS software for interactive genome maps.
- Represented genome features and attributes as spatial objects and registered layers.
Main Results:
- Implemented an interactive mouse genome feature map using GenoSIS.
- GenoSIS allows dynamic generation of custom genome maps based on complex queries.
- Demonstrated powerful visualization and query capabilities by applying GIS technology to genomics.
Conclusions:
- GIS mapping tools can be effectively utilized for displaying and exploring genome data.
- The GenoSIS approach is organism-independent and applicable to various chromosome types.
- GenoSIS offers unique dynamic map generation capabilities for complex genome queries, surpassing existing browsers.
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...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:28Introduction to GIS
Geographic Information Systems (GIS) are tools for storing, analyzing, and displaying spatial data alongside related attributes. Unlike traditional information systems that address general queries, GIS incorporates spatial components, enabling users to answer "where" and "how far." For example, GIS can process housing data linked to geographic locations like zip codes, allowing insights into population density or housing distribution through thematic maps.GIS integrates technologies such as...
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...