How to simply download sequence for a specified region?

[Curtis, David]

Hi all.

I just want to download human reference sequence for a defined region.

If I use the browser I can see the bases and the track seems to be called "complement bases". But if I use the Table Browser I cannot find any track called this. In fact, I cannot find any track which if I download it then I get all the bases in the region. E.g. some tracks might just be "variants" or whatever. I cannot find any way to simply get raw sequence.

If there is a way to do this it would be helpful to explain it more clearly.

Regards

 - Dave Curtis

[Robert Kuhn]

David,

In the top bluebar, find View>DNA. That will give the seq of the region in the window. 

Can also RT-click an annotation.

   ..b0b kuhn

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

As Bob shares, you can use the bluebar menu (View --> DNA) to download the genomic sequence. If you are looking for a programmatic approach, there is also a REST API that you can use to obtain the genomic sequence, e.g.:

api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678

The full list of parameters for the API can be found on the following help page:

https://genome.ucsc.edu/goldenPath/help/api.html

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Jairo Navarro
UCSC Genome Browser

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[Curtis, David]

Hi.

Thanks for these responses. Obviously it's very quick and easy when one knows how. But the documentation I could find did not explain this at all because it gave me the idea that I should be starting with the Table Browser. It would be good to review the documentation.

Best wishes

- Dave

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From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: 01 October 2025 22:10
To: Curtis, David <d.cu...@ucl.ac.uk>
Cc: UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>; Robert Kuhn <ku...@soe.ucsc.edu>
Subject: Re: [genome] How to simply download sequence for a specified region?

 

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