4.6 Ideogram Viewer

4.6.1 Usage

The Ideogram Viewer provides a visualization of the detailed positions of telomeres, centromeres, and gaps in the genome. It also allows users to compare the positions of centromeres in different genomes.

4.6.1 How to predict the position

Telomere - The telomere is the end of a chromosome, which is essential for maintaining the stability of the chromosome and preventing the loss of genetic information. The telomere is composed of a series of repetitive DNA sequences, such as CCCTAAA in plants. So, the telomere can be predicted by searching for the telomere sequence in the genome. Here, we screened the CCCTAAA sequence in the end of the chromosome. If the repeat count is greater than 20, we consider it as a telomere.

Centromere - The centromere is the region of a chromosome where the two sister chromatids are joined. The centromere is essential for the segregation of chromosomes during cell division. The centromere is composed of a series of tandem repetitive (TR) DNA sequences. For example, the centromere of Arabidopsis thaliana contains millions of base pairs of satellite repeat sequences, with a single satellite repeat sequence containing around 180 base pairs, so these repeat sequences are called CEN180. Here, we screened the CENXXX sequence in the genome. If the proportion of these CENXXX occupying the repetitive sequence is greater than 10%, we consider it as a candidate centromere. From all the candidate centromeres, we choose the longest region as the centromere.

Gaps - The gap is the region of a chromosome where the sequence is missing (like ATCGNNNNNNNNNNCGAT). The gap is usually caused by the difficulty in sequencing or assembling the region. We can search for the NNNNNNNNNN sequence in the genome. Continuous Ns are considered as a gap.