Department of Bioinformatics and Computational Biology

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Ideogram Viewer

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DescriptionAn interactive tool for viewing the location and annotation of genes on human chromosomes
Development Information
Current version1.0.8
PlatformsWeb application
LicenseNot Required
Last updatedJuly 29, 2016
Help and Support
Contact Bradley M. Broom 

Ideogram Viewer


Ideograms provide a schematic representation of chromosomes. They are used to show the relative size of the chromosomes and their characteristic banding patterns.

We have developed an interactive viewer to show the location of the requested genes and microRNAs on human chromosomes. We collected a set of human oncogenes and tumor suppressor genes from different resources that can be chosen to display on chromosomes.

Viewer Features

Feature Description

An example of displaying the gene markers and annotations:

An example of selecting a genomic region on a chromosome:

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Data sources

Cytoband color scheme

Each cytoband has a staining color and a banding pattern. Cytogenetic bands also provide potential predictions of the structural characteristics of a chromosome. Ideogram viewer uses cytoband colors consistent with Bioconductor’s R package, biovizBase: biovizBase .

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Legend color scheme

The genes and microRNAs are indicated by the colored solid or dashed lines in the viewer.

Genes or microRNA Ids from query parameters in the website url:

Oncogenes and Suppressor genes from data files:

All labels for gene symbols or microRNA IDs by default are in black text. If a gene is from the parameter list and is an oncogene or a suppressor, the label is orange (for oncogene) or lime green (for suppressor).

Browser compatibility

This application will not work on all internet browsers. We have tested it on the following browsers:

How to capture high quality images for publication

Please refer to this page How to capture high quality images for publication


Rong Yao, Chris Wakefield, Bradley Broom. We thank Kevin Coombes for creating the geneSmash web service for gene annotations. We thank the UCSC Genome Browser Project Team for providing the web resource to download cytoband data.

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