Segmental duplications track

[Emma]

I'm having trouble interpreting the notation used for these duplications.

Where is the DUP being inserted? Is there a way to know the coordinates of the original vs duplicated (homologous) segments?

Is it being inserted at the start position or end position of each block?

Also how are the arrows (for the strand) determined?

[Jairo Navarro Gonzalez]

Hi Emma,

Thank you for your question about the Segmental Duplications track. The track shows regions of the genome that appear in two or more copies with ≥90% identity and ≥1kb in length.

For your specific questions:
1. The track displays the locations of duplicated segments, not insertion points. Each colored block represents a duplicated region. Colors are used to distinguish levels of similarity.
2. To find coordinates of homologous segments, click on individual items in the track - this will show you all genomic locations where that particular duplication occurs.
3. The blocks show where the duplications exist in the reference genome, not where they were "inserted."
4. Arrow directions indicate the orientation/strand of each duplicated segment relative to its homologous copies.

For more detailed information about methodology and interpretation, please see the track description page by clicking on the track name. The paper in the references section can explain the methodology used to generate the track data:

https://genome.cshlp.org/content/11/6/1005.long

Feel free to also search the mailing list archives to find other previously answered questions about segmental duplications:

https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=segmental%20duplications

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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[Emma]

That makes sense. Thank you!