Cytogenetic ideograms

An ideogram, also called a cytogenetic ideogram, is a chromosome map with numbered banding patterns that shows the relationship between the two chromosome arms and the centromere. Users of the UCSC Genome Browser ( are most likely familiar with the use of cytogenetic ideogram in the UCSC Genome Browser. Ideograms can be imported into the Workbench (from UCSC) and be used in track lists to provide an overview of the analyzed data in context of the individual chromosomes. An example is shown in figure 11.9.

Image ideogram_in_genomebrowserview
Figure 11.9: The ideogram is particularly useful when used in combination with other tracks in a track list. In this figure the ideogram is highlighted with a red box.

The ideogram can be imported into CLC Genomics Workbench via the download function found in the upper right corner of the Workbench.

        Download | Download Reference Genome Data (Image annotate_tracks_16_n_p) | select "Chromosome bands (ideogram)"

For a description of how to do this please refer to Download reference genome data. The imported ideograms can be found in the Navigation Area at the destination that was specified in the download wizard. The ideograms are always accompanied by a reference sequence (see figure 11.10).

Image downloaded_ideograms
Figure 11.10: The ideograms and the reference sequence in the Navigation Area.